diff --git a/.gitignore b/.gitignore index 827d30c0..462885f4 100755 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,9 @@ public/* .DS_Store /.venv transcript.en.vtt +.idea/* +.hugo_build.lock +resources/* __pycache__ __pycache__/ __pycache__/*.pyc diff --git a/Dockerfile b/Dockerfile index f28f7b67..4e653452 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,3 +1,4 @@ FROM klakegg/hugo:ext-alpine -RUN apk add git +RUN apk add git && \ + git config --global --add safe.directory /src diff --git a/__pycache__/vfbterms.cpython-314.pyc b/__pycache__/vfbterms.cpython-314.pyc deleted file mode 100644 index dc6188b7..00000000 Binary files a/__pycache__/vfbterms.cpython-314.pyc and /dev/null differ diff --git a/content/en/about/cite.md b/content/en/about/cite.md deleted file mode 100644 index 3c52c6f0..00000000 --- a/content/en/about/cite.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -title: "VFB citation bibtex" -date: 2023-01-30 -weight: 5000 ---- -```BibTeX -@article{Court_2023, - doi = {10.3389/fphys.2023.1076533}, - url = {https://doi.org/10.3389/fphys.2023.1076533}, - year = 2023, - month = {jan}, - publisher = {Frontiers Media {SA}}, - volume = {14}, - author = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland}, - title = {Virtual Fly Brain{\textemdash}An interactive atlas of the Drosophila nervous system}, journal = {Frontiers in Physiology}} -``` diff --git a/content/en/about/citeus.md b/content/en/about/citeus.md index d676295f..7dbe02e0 100644 --- a/content/en/about/citeus.md +++ b/content/en/about/citeus.md @@ -24,8 +24,8 @@ Court, Robert, et al. "Virtual Fly Brain—An Interactive Atlas of the Drosophil Court, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. "Virtual Fly Brain—An interactive atlas of the Drosophila nervous system." *Frontiers in Physiology* 14, (2023). https://doi.org/10.3389/fphys.2023.1076533. ### BibTeX -```bibtex -@article{10.3389/fphys.2023.1076533, +```BibTeX +@article{Court_2023, author = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland}, title = "{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}", journal = {Frontiers in Physiology}, @@ -35,7 +35,7 @@ Court, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, Mc month = {jan}, abstract = "{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}", issn = {1664-042X}, - doi = {https://doi.org/10.3389/fphys.2023.1076533}, + doi = {10.3389/fphys.2023.1076533}, url = {https://doi.org/10.3389/fphys.2023.1076533}, } ``` diff --git a/content/en/about/collaborators.md b/content/en/about/collaborators.md index 49d31cbf..04e8d64a 100644 --- a/content/en/about/collaborators.md +++ b/content/en/about/collaborators.md @@ -16,5 +16,6 @@ weight: 500 [![flybase.gif](https://v2.virtualflybrain.org/images/vfb/project/logos/flybase.gif)](http://www.flybase.org/) - **Expression data** is collaboratively curated by VFB and [FlyBase](http://www.flybase.org/). - Phenotype data is curated by FlyBase. Expression and phenotype data displayed on VFB is stored and maintained by FlyBase. + **Expression data** is collaboratively curated by VFB and [FlyBase](http://www.flybase.org/) and stored and maintained at FlyBase. + + **Phenotype data** is curated, stored, and maintained by FlyBase. diff --git a/content/en/about/funding.md b/content/en/about/funding.md index 13a0b470..77e9cff9 100644 --- a/content/en/about/funding.md +++ b/content/en/about/funding.md @@ -4,13 +4,13 @@ date: 2025-06-11 weight: 500 tags: [VFB,funding] categories: [funding,acknowledgements,who we are] -description: "VirtualFlyBrain has been supported by grants from multiple UK research councils and charitable foundations since 2009." +description: "Virtual Fly Brain has been supported by grants from multiple UK research councils and charitable foundations since 2009." --- ## Current Funding (2022-2027) **Wellcome Trust Grant 223741/Z/21/Z** - Duration: April 1, 2022 to March 31, 2026 (extended to March 31, 2027) -- Supporting ongoing VirtualFlyBrain development and maintenance +- Supporting ongoing Virtual Fly Brain development and maintenance ## Historical Funding @@ -50,17 +50,16 @@ description: "VirtualFlyBrain has been supported by grants from multiple UK rese ## Institutional Partners -VirtualFlyBrain is a collaborative project between: +Virtual Fly Brain is a collaborative project between: - **University of Edinburgh** - School of Informatics -- **University of Cambridge** - Multiple departments including Genetics, Physiology Development & Neuroscience, and Zoology -- **EMBL's European Bioinformatics Institute (EMBL-EBI)** - Hinxton, UK +- **University of Cambridge** - Departments of Physiology Development & Neuroscience, and Zoology - **Wellcome Sanger Institute** - Hinxton, UK - **MRC Laboratory for Molecular Biology** - Cambridge ## Data Partnerships -VirtualFlyBrain integrates data from multiple sources through collaborative partnerships rather than direct funding arrangements: +Virtual Fly Brain integrates data from multiple sources through collaborative partnerships rather than direct funding arrangements: - FlyBase Consortium - FlyCircuit Project (National Tsing Hua University, Taiwan) @@ -69,7 +68,7 @@ VirtualFlyBrain integrates data from multiple sources through collaborative part ## Site Visualization Tools -VirtualFlyBrain utilizes multiple visualization technologies: +Virtual Fly Brain utilizes multiple visualization technologies: **Geppetto Framework** - Open source 3D visualization platform co-developed with MetaCell Corporation diff --git a/content/en/blog/releases/geppetto/_index.md b/content/en/about/geppetto.md similarity index 99% rename from content/en/blog/releases/geppetto/_index.md rename to content/en/about/geppetto.md index 4ce4f55a..375f657b 100644 --- a/content/en/blog/releases/geppetto/_index.md +++ b/content/en/about/geppetto.md @@ -1,7 +1,7 @@ --- title: "Geppetto" linkTitle: "Geppetto" -weight: 21 +weight: 800 tags: [Geppetto,MetaCell] description: > The ultimate neuroscience platform. diff --git a/content/en/about/members.md b/content/en/about/members.md index d058a0aa..73cbd857 100644 --- a/content/en/about/members.md +++ b/content/en/about/members.md @@ -1,93 +1,77 @@ --- -title: Virtual Fly Brain Members and Their Contributions -description: "Meet the interdisciplinary team behind Virtual Fly Brain, including developers, curators, ontology experts, and researchers from leading UK institutions who collaborate to maintain and enhance this comprehensive Drosophila neuroscience resource." +title: The Virtual Fly Brain Team +description: "Meet the interdisciplinary team behind Virtual Fly Brain based in leading UK institutions. Our collaborative approach brings together expertise in informatics, neuroscience, ontology development, and data curation to maintain and enhance this comprehensive Drosophila neuroscience resource." tags: [VFB,staff] categories: [acknowledgements,who we are] weight: 400 --- -# Virtual Fly Brain Team +## Current Team Members -Virtual Fly Brain is developed and maintained by an interdisciplinary team of researchers, developers, and curators across multiple UK institutions. Our collaborative approach brings together expertise in informatics, neuroscience, ontology development, and data curation. +- [Robert Court](https://www.inf.ed.ac.uk/people/staff/Robert_Court.html) (Lead DevOps) [1] +- [Clare Pilgrim](https://orcid.org/0000-0002-1373-1705) (Ontology Editor/Curator) [2] +- [Alex McLachlan](https://orcid.org/0000-0002-5214-8125) (Curator/UX Tester) [2] +- [Gillian Millburn](https://orcid.org/0000-0002-1139-1145) (Senior Curator) [2] -## 3D Viewer, Online Tools, Server, and Website +- [Douglas Armstrong](https://www.inf.ed.ac.uk/people/staff/James_Armstrong.html) (Current Project PI) [1] +- [Nick Brown](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Current Project PI) [2] +- [Greg Jefferis](http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/gregory-jefferis/) (Current Project PI) [4,5] +- [David Osumi-Sutherland](https://orcid.org/0000-0002-7073-9172) (Current Project Co-I) [3] +- [Marta Costa](http://www.neuroscience.cam.ac.uk/directory/profile.php?mcosta) (Current Project Co-I) [4] - - - - -### Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh - -- [Robert Court](https://www.inf.ed.ac.uk/people/staff/Robert_Court.html) (Lead DevOps) -- [Douglas Armstrong](https://www.inf.ed.ac.uk/people/staff/James_Armstrong.html) (Current Project PI) -- Nestor Milyaev (2009-2012) - -## Ontology Editing, FlyBase Support, and Data Annotation - - - - - -### Department of Genetics, University of Cambridge -- [Cahir O'Kane](http://www.neuroscience.cam.ac.uk/directory/profile.php?cokane) (Current Project PI) -- Michael Ashburner (Original PI and Grant Holder) -- Simon Reeve (2009-2011) -- Nicole Staudt (2015-2016) -- Alex Holmes (2017-2019) +## Past Team Members +- Nestor Milyaev (2009-2012) [1] +- Alex Holmes (2017-2019) [2] +- [Aoife Larkin](https://orcid.org/0000-0003-4970-5901) (2017-2019) [2] +- [Huseyin Kir](https://www.ebi.ac.uk/people/person/huseyin-kir/) (2021-2024) [6] +- [Nico Matentzoglu](https://orcid.org/0000-0002-7356-1779) (2018-2022) [6] +- Simon Reeve (2009-2011) [7] +- Nicole Staudt (2015-2016) [7] -### Department of Physiology, Development and Neuroscience +- [Helen Parkinson](https://www.ebi.ac.uk/about/people/helen-parkinson) (Former PI) [6] +- [Cahir O'Kane](http://www.neuroscience.cam.ac.uk/directory/profile.php?cokane) (Former PI) [7] +- [Michael Ashburner](https://orcid.org/0000-0002-6962-2807) (Original PI and Grant Holder) [7] -- [Clare Pilgrim](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Senior Ontology Editor/Curator) -- [Alex McLachlan](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Curator/UX Tester) -- [Aoife Larkin](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Curator) -- [Gillian Millburn](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Senior Curator) -- [Nick Brown](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Current Project PI) +### Affiliations +1. Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh +2. Department of Physiology, Development and Neuroscience +3. Wellcome Sanger Institute, Cambridge +4. Department of Zoology, University of Cambridge +5. MRC Laboratory of Molecular Biology, Cambridge +6. European Bioinformatics Institute (EMBL-EBI), Cambridge +7. Department of Genetics, University of Cambridge -### Department of Zoology, University of Cambridge +## [MetaCell](http://www.metacell.us) -- [Marta Costa](http://www.neuroscience.cam.ac.uk/directory/profile.php?mcosta) (Current Project Co-I) - -## Image Processing, Registration, and NBLAST Neuron Search +MetaCell collaborates with Virtual Fly Brain on the development and enhancement of the open source [Geppetto](http://www.geppetto.org) visualization platform that powers our 3D brain viewer. - - +--- + + + -### MRC Laboratory of Molecular Biology, Cambridge - -- [Greg Jefferis](http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/gregory-jefferis/) (Current Project PI) - -## Schema Development & Web Development - - - + + -### Wellcome Sanger Institute, Cambridge + + + -- [David Osumi-Sutherland](https://www.linkedin.com/in/osumisutherland) (Current Project Co-I) + + + - - - -### European Bioinformatics Institute (EMBL-EBI), Cambridge - -- [Huseyin Kir](https://www.ebi.ac.uk/people/person/huseyin-kir/) (Developer) -- [Nico Matentzoglu](https://www.researchgate.net/profile/Nicolas_Matentzoglu2) (Developer) -- [Helen Parkinson](https://www.ebi.ac.uk/about/people/helen-parkinson) (Current Project PI) - -## Software Engineering, Geppetto Customisation, Graphics Design + + - + -### [MetaCell](http://www.metacell.us) - -MetaCell collaborates with Virtual Fly Brain on the development and enhancement of the open source [Geppetto](http://www.geppetto.org) visualization platform that powers our 3D brain viewer. - --- For questions about team members or collaboration opportunities, please [contact us](mailto:data@virtualflybrain.org). diff --git a/content/en/about/whatisvfb.md b/content/en/about/whatisvfb.md index 493d848a..5d4db4a5 100644 --- a/content/en/about/whatisvfb.md +++ b/content/en/about/whatisvfb.md @@ -1,9 +1,9 @@ --- title: What is Virtual Fly Brain? description: Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster. -weight: 100 +weight: 10 --- Welcome to **Virtual Fly Brain (VFB)** - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of _Drosophila melanogaster_. Our goal is to make it easier for researchers to find relevant anatomical information and reagents. -We integrate the neuroanatomical and expression data from the published literature, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons, and compare image data on our [3D Viewer](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto). +We integrate the neuroanatomical and expression data from the published literature, and align image datasets onto the same nervous system [templates](/docs/data/templates), making it possible to run cross searches, find similar neurons, and compare image data on our [3D Viewer](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto). diff --git a/content/en/blog/news/_index.md b/content/en/blog/news/_index.md index 9b5a0f93..bfc145af 100644 --- a/content/en/blog/news/_index.md +++ b/content/en/blog/news/_index.md @@ -1,6 +1,6 @@ --- -title: "News about Virtual Fly Brain (VFB)" +title: "Virtual Fly Brain News" linkTitle: "News" weight: 20 cascade: diff --git a/content/en/blog/news/neurofly2026.md b/content/en/blog/news/neurofly2026.md index 0312712b..57246219 100644 --- a/content/en/blog/news/neurofly2026.md +++ b/content/en/blog/news/neurofly2026.md @@ -8,6 +8,6 @@ description: > The 21st Biennial European Drosophila Neurobiology Conference, NeuroFly 2026, will be held at the University of Cologne, Germany, from September 7th to 11th, 2026. This conference continues the tradition of bringing together researchers from around the world to discuss the latest advancements in Drosophila neurobiology, including studies on neuronal circuits, synapses, connectome, signal transmission, behavior, development, and more. The event emphasizes interdisciplinary interactions in an inclusive environment, featuring a mix of invited talks and abstracts from both junior and senior researchers. -Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/Tutorials/APIs/Connectome/tools) and [APIs](/docs/Tutorials/APIs/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation. +Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as the one at [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/past-workshops/connectome/tools) and [APIs](/docs/tutorials/apis/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation. For more information about NeuroFly 2026, including registration, abstract submission, and program details, visit the official website at [https://neurofly.org/home/](https://neurofly.org/home/) or the 2026 conference page at [https://neurofly.org/y2026/](https://neurofly.org/y2026/). diff --git a/content/en/blog/ontologies/_index.md b/content/en/blog/ontologies/_index.md new file mode 100755 index 00000000..55b03261 --- /dev/null +++ b/content/en/blog/ontologies/_index.md @@ -0,0 +1,20 @@ +--- +title: "Ontologies and Vocabularies Used in the Current VFB Release" +linkTitle: "Ontologies" +tags: [ontologies,annotation] +date: 2021-12-24 +categories: [ontologies,annotations] +weight: 50 +Description: > + The external ontologies and controlled vocabulary terms used to create VFB. +cascade: +- type: "docs" + _target: + path: "/**" +--- + +These are mostly open source projects and contributions are welcome. VFB actively maintains FBbt, FBcv, dpo and FBdv and contributes to FlyBase and RO. + + + + diff --git a/content/en/blog/releases/ontologies/bfo/_index.md b/content/en/blog/ontologies/bfo/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/bfo/_index.md rename to content/en/blog/ontologies/bfo/_index.md diff --git a/content/en/blog/releases/ontologies/caro/_index.md b/content/en/blog/ontologies/caro/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/caro/_index.md rename to content/en/blog/ontologies/caro/_index.md diff --git a/content/en/blog/releases/datasets/_index.md b/content/en/blog/ontologies/datasets/_index.md similarity index 100% rename from content/en/blog/releases/datasets/_index.md rename to content/en/blog/ontologies/datasets/_index.md diff --git a/content/en/blog/releases/ontologies/dpo/_index.md b/content/en/blog/ontologies/dpo/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/dpo/_index.md rename to content/en/blog/ontologies/dpo/_index.md diff --git a/content/en/blog/releases/ontologies/fbbi/_index.md b/content/en/blog/ontologies/fbbi/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/fbbi/_index.md rename to content/en/blog/ontologies/fbbi/_index.md diff --git a/content/en/blog/releases/ontologies/fbbt/_index.md b/content/en/blog/ontologies/fbbt/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/fbbt/_index.md rename to content/en/blog/ontologies/fbbt/_index.md diff --git a/content/en/blog/releases/ontologies/fbcv/_index.md b/content/en/blog/ontologies/fbcv/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/fbcv/_index.md rename to content/en/blog/ontologies/fbcv/_index.md diff --git a/content/en/blog/releases/ontologies/fbdv/_index.md b/content/en/blog/ontologies/fbdv/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/fbdv/_index.md rename to content/en/blog/ontologies/fbdv/_index.md diff --git a/content/en/blog/releases/ontologies/flybase/_index.md b/content/en/blog/ontologies/flybase/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/flybase/_index.md rename to content/en/blog/ontologies/flybase/_index.md diff --git a/content/en/blog/releases/ontologies/geno/_index.md b/content/en/blog/ontologies/geno/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/geno/_index.md rename to content/en/blog/ontologies/geno/_index.md diff --git a/content/en/blog/releases/ontologies/go/_index.md b/content/en/blog/ontologies/go/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/go/_index.md rename to content/en/blog/ontologies/go/_index.md diff --git a/content/en/blog/releases/ontologies/ioa/_index.md b/content/en/blog/ontologies/ioa/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/ioa/_index.md rename to content/en/blog/ontologies/ioa/_index.md diff --git a/content/en/blog/releases/ontologies/ncbitaxon/_index.md b/content/en/blog/ontologies/ncbitaxon/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/ncbitaxon/_index.md rename to content/en/blog/ontologies/ncbitaxon/_index.md diff --git a/content/en/blog/releases/ontologies/obi/_index.md b/content/en/blog/ontologies/obi/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/obi/_index.md rename to content/en/blog/ontologies/obi/_index.md diff --git a/content/en/blog/releases/ontologies/pato/_index.md b/content/en/blog/ontologies/pato/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/pato/_index.md rename to content/en/blog/ontologies/pato/_index.md diff --git a/content/en/blog/releases/ontologies/pco/_index.md b/content/en/blog/ontologies/pco/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/pco/_index.md rename to content/en/blog/ontologies/pco/_index.md diff --git a/content/en/blog/releases/ontologies/ro/_index.md b/content/en/blog/ontologies/ro/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/ro/_index.md rename to content/en/blog/ontologies/ro/_index.md diff --git a/content/en/blog/releases/ontologies/so/_index.md b/content/en/blog/ontologies/so/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/so/_index.md rename to content/en/blog/ontologies/so/_index.md diff --git a/content/en/blog/releases/ontologies/uberon/_index.md b/content/en/blog/ontologies/uberon/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/uberon/_index.md rename to content/en/blog/ontologies/uberon/_index.md diff --git a/content/en/blog/releases/ontologies/vfb/_index.md b/content/en/blog/ontologies/vfb/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/vfb/_index.md rename to content/en/blog/ontologies/vfb/_index.md diff --git a/content/en/blog/releases/ontologies/wbphenotype/_index.md b/content/en/blog/ontologies/wbphenotype/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/wbphenotype/_index.md rename to content/en/blog/ontologies/wbphenotype/_index.md diff --git a/content/en/blog/releases/ontologies/zp/_index.md b/content/en/blog/ontologies/zp/_index.md similarity index 100% rename from content/en/blog/releases/ontologies/zp/_index.md rename to content/en/blog/ontologies/zp/_index.md diff --git a/content/en/blog/releases/_index.md b/content/en/blog/releases/_index.md index 830f6d47..c1052ee7 100644 --- a/content/en/blog/releases/_index.md +++ b/content/en/blog/releases/_index.md @@ -3,7 +3,7 @@ title: "Release Information" linkTitle: "Releases" weight: 20 description: > - The Virtual Fly Brain (VFB) site consists of open source software projects we contribute to and actively develop as well as ontologies that we actively curate into and utilise in building the data for our servers. Here we provide details of these. + Virtual Fly Brain (VFB) is regularly updated with new data and software improvements. Information about the latest release can be found here. cascade: - type: "docs" _target: diff --git a/content/en/blog/releases/catmaid/_index.md b/content/en/blog/releases/catmaid/_index.md deleted file mode 100644 index dcd0a357..00000000 --- a/content/en/blog/releases/catmaid/_index.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: "Catmaid" -linkTitle: "Catmaid" -weight: 20 -description: > - The Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is a web companion to the TrakEM2 software (Cardona, 2006) for management, registration and analysis of large-scale ssTEM datasets -cascade: -- type: "docs" - _target: - path: "/**" ---- - -## Documentation - -[CATMAID documentation](https://catmaid.readthedocs.io/en/stable/) - -[@catmaid](https://twitter.com/catmaid) - -## Intro - -{{< youtube id="CZpaTCuSQao" autoplay="true" title="A video introduction to catmaid software for connectomics from lead developer Tom Kazimiers hosted by the NEUBIAS Academy" >}} - -## CATMAID Datasets Hosted by VFB - -Virtual Fly Brain (VFB) hosts several CATMAID instances for exploring connectomic reconstruction data. These datasets provide access to neuroanatomical data from various Drosophila electron microscopy projects. Full details are available on our hosted pages: - -### Adult Brain -- [FAFB (Adult Fly Brain)](/about/hosted/fafb-catmaid/) - Complete EM volume of an adult Drosophila melanogaster brain with manually traced neurons -- [FANC (Female Adult Nerve Cord)](/about/hosted/fanc-catmaid/) - Adult female ventral nerve cord with reconstructions in both original and template space - -### Larval Brain -- [L1EM (First Instar Larva)](/about/hosted/l1em-catmaid/) - Complete EM volume of a Drosophila first instar larva brain with manually traced neurons - -#### Comparative Studies -- [IAV-ROBO](/about/hosted/iav-robo-catmaid/) - Mechanosensory circuit study with shifted mechanosensory projections -- [IAV-TNT](/about/hosted/iav-tnt-catmaid/) - Control dataset for comparative mechanosensory circuit studies - -Each dataset includes browser-based visualization of EM data, neuron reconstructions, connectivity information, and programmatic access via APIs. VFB ensures the long-term availability of these resources to the research community. diff --git a/content/en/blog/releases/flylight/index.md b/content/en/blog/releases/flylight/index.md deleted file mode 100644 index 98a62410..00000000 --- a/content/en/blog/releases/flylight/index.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -title: "Janelia FlyLight" -linkTitle: "FlyLight" -weight: 20 -tags: ["Split","Expression_pattern","transgene","FlyLight","Janelia","Larval","MCFO","NeuronBridge"] -description: > - The FlyLight Project produces large anatomical data sets and highly characterized collections of GAL4, LexA and Split-GAL4 drivers in order to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system. -cascade: -- type: "docs" - _target: - path: "/**" ---- - -## Documentation - -[FlyLight Project Homepage](https://www.janelia.org/project-team/flylight) - -## Intro - -FlyLight makes its primary data available via VFB as well as through dedicated websites for expression patterns of Generation 1 GAL4 and LexA lines and for split-GAL4 lines. Generation 1, split hemidriver, and stable split combination lines are available primarily from the Bloomington Stock Center. Stable split lines can also be requested via the split-GAL4 website. - -## FlyLight Data and Resources - -While FlyLight's data is intergrated & indexed on [VFB](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=VFB_00101567,AllDatasets) and direct link out provided to the images on these sites they can be directly searched: - -[Browse the Generation 1 GAL4 expression patterns](https://flweb.janelia.org/) - -[Browse the Generation 1 MCFO (single neuron) patterns](https://gen1mcfo.janelia.org/) - -[Browse the Split-GAL4 Expression Patterns](https://splitgal4.janelia.org/) - -[Browse the Raw Image Collection](https://flylight-raw.janelia.org/cgi-bin/raw.cgi) - -[Search light and EM neurons - NeuronBridge](https://neuronbridge.janelia.org/) - -[VFB hosted Larval Expression Patterns](https://raw.larval.flylight.virtualflybrain.org/) diff --git a/content/en/blog/releases/ontologies/_index.md b/content/en/blog/releases/ontologies/_index.md deleted file mode 100755 index fc081b13..00000000 --- a/content/en/blog/releases/ontologies/_index.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: "Ontologies" -linkTitle: "Ontologies" -tags: [ontologies,annotation] -date: 2021-12-24 -categories: [ontologies,annotations] -weight: 50 -Description: > - Here we list all the ontologies used to create VFB. -cascade: -- type: "docs" - _target: - path: "/**" ---- - -Most we also actively contribute to and actively maintain but are all open source projects so feel free to review and follow the guidance provided to contribute. - - - - diff --git a/content/en/docs/APIs/_index.md b/content/en/docs/APIs/_index.md index 3c0965d1..425ab62a 100644 --- a/content/en/docs/APIs/_index.md +++ b/content/en/docs/APIs/_index.md @@ -16,7 +16,7 @@ VFB provides access to its data through several APIs and databases. The core dat - **VFB Web Interface**: [https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto) - User-friendly web interface for browsing and querying VFB data **For Programmatic Access:** -- **VFBconnect Library**: [https://vfb-connect.readthedocs.io/](https://vfb-connect.readthedocs.io/) - Python library that provides high-level access to VFB data and queries. See also: [VFB API Tutorial](Tutorials/APIs/0_VFB_API_overview.md) +- **VFBconnect Library**: [https://vfb-connect.readthedocs.io/](https://vfb-connect.readthedocs.io/) - Python library that provides high-level access to VFB data and queries. See also: [VFB API Tutorial](/docs/tutorials/apis/VFB_API_overview.md) **For Advanced Data Access:** - **Direct APIs** (documented below): Low-level access to underlying databases and reasoning services diff --git a/content/en/docs/Examples/Circuit diagram of the mushroom body/_index.md b/content/en/docs/Anatomy Diagrams/Circuit diagram of the mushroom body/_index.md similarity index 100% rename from content/en/docs/Examples/Circuit diagram of the mushroom body/_index.md rename to content/en/docs/Anatomy Diagrams/Circuit diagram of the mushroom body/_index.md diff --git a/content/en/docs/Anatomy Diagrams/_index.md b/content/en/docs/Anatomy Diagrams/_index.md new file mode 100755 index 00000000..c5ad4713 --- /dev/null +++ b/content/en/docs/Anatomy Diagrams/_index.md @@ -0,0 +1,11 @@ + +--- +title: "Anatomy Diagrams" +linkTitle: "Anatomy Diagrams" +weight: 50 +date: 2026-01-19 +description: > + Diagrams associated with anatomy terms from the Drosophila Anatomy Ontology. +--- + + diff --git a/content/en/docs/Concepts/_index.md b/content/en/docs/Concepts/_index.md index 0952eb2a..413cb473 100644 --- a/content/en/docs/Concepts/_index.md +++ b/content/en/docs/Concepts/_index.md @@ -3,6 +3,6 @@ title: "Concepts" linkTitle: "Concepts" weight: 4 description: > - Details of concepts or terms used in Virtual Fly Brain + Details of concepts or terms used in Virtual Fly Brain. --- diff --git a/content/en/docs/Concepts/nblast.md b/content/en/docs/Concepts/nblast.md index a1da1d5a..61d5fc1a 100644 --- a/content/en/docs/Concepts/nblast.md +++ b/content/en/docs/Concepts/nblast.md @@ -48,12 +48,7 @@ VFB NBLAST scores cover: ### Accessing NBLAST queries -NBLAST similarity searches are available directly in the VFB interface: - -1. Navigate to any individual neuron or split-GAL4 image page -2. Scroll to the term info panel -3. Look for NBLAST query options (only appears if results are available) -4. Click to see ranked lists of morphologically similar items + See [Similarity Score Queries Guide](/docs/tutorials/website/similarityscore/) for details of how to find NBLAST similarity queries in the VFB interface. ### Interpreting results @@ -96,6 +91,6 @@ NBLAST results on VFB can be: ## Further reading -- [NBLAST tutorial](/docs/tutorials/apis/4_nblast/) - Detailed programming tutorial +- [NBLAST tutorial](/docs/tutorials/apis/nblast/) - Detailed programming tutorial - [Original NBLAST paper](https://doi.org/10.1016/j.neuron.2016.06.012) - Costa et al., 2016 - [VFB NBLAST announcement](/blog/2025/05/29/new-precomputed-neuron-and-expression-pattern-similarity-scores-on-vfb/) - Recent updates and expanded coverage diff --git a/content/en/docs/Concepts/splits.md b/content/en/docs/Concepts/splits.md index 7f71920d..747f6d7a 100644 --- a/content/en/docs/Concepts/splits.md +++ b/content/en/docs/Concepts/splits.md @@ -1,19 +1,30 @@ --- -title: "Split Expression" -linkTitle: "Split Expression" +title: "Split Driver Expression Patterns" +linkTitle: "Split Driver Expression" categories: ["overview","help"] tags: ["Split","Expression_pattern","transgene","FlyLight"] weight: 30 description: > - This techniques works by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes. + Split driver expression patterns in Virtual Fly Brain. --- -Thousands of hemi-driver transgenes are now available, meaning that millions of combinations/[splits](/tags/split/) are possible, each targeting some precise subset of the 10s-100s of thousands of neurons in a fly Central Nervous System (CNS). Finding the right combination for an experiment is a serious bottleneck for researchers. +Split drivers comprise at least two partial transcription factors that can reconstitute an active transcription factor when expressed in the same cell. By using different regulatory regions for each component, functional driver expression can be restricted to the intersection of the expression patterns of these regulatory regions. A wide range of regulatory regions have been combined with transcription factor DNA binding domains (DBDs) and Activation Domains (ADs) to form thousands of distinct constructs, referred to as hemidrivers. Millions of combinations are therefore possible, each targeting some precise subset of the many thousands of neurons in the Drosophila nervous system. -[FlyBase](https://flybase.org/) & [Virtual Fly Brain (VFB)](https://virtualflybrain.org) solve this problem by curating information and images recording where expression is driven by combinations of hemi-drivers. Each combination gets a standard name on VFB reflecting the names of the component hemidrivers (see figure below) and is also associated with any short names for the combination used in the literature (e.g. "[P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFBexp_FBtp0123314FBtp0119891)" has_exact_synonym: SS02256") +A split-GAL4 expression pattern at the intersection of the expression patterns of two hemidrivers. -This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes. +Researchers can identify split drivers for neurons of interest from the `Targeting Splits` section of a cell type [Term Info](/docs/website-features/terminfo) page or by using [similarity scores](/docs/tutorials/website/similarityscore/) from a single neuron image. It is also possible to [search](/docs/website-features/search_query) directly for particular hemidrivers and combinations. -We use programmatic methods to generate expression statements for hemi-driver combinations with [FlyLight](https://www.janelia.org/project-team/flylight) image data hosted by [VFB](https://virtualflybrain.org). Combinations are validated against a local copy of the FlyLight dataset and a structured user readable comment is generated as part of the expression statement. These hyperlink to the partner hemi-driver in [FlyBase](https://flybase.org/), contain the strain designation (where available) and can be automatically parsed by [Virtual Fly Brain](](https://virtualflybrain.org)) to attach expression and genetic data to a node representing the intersection. +Targeting Splits section of cell type Term Info page. + +Similar to [non-split drivers](/docs/concepts/transgene), VFB contains images and curated information about expression patterns for combinations. Each combination gets a standard name in VFB, reflecting the names of the component hemidrivers and any short names for the combination from the literature are added as synonyms (e.g. "[P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFBexp_FBtp0123314FBtp0119891)" has_exact_synonym: SS02256"). split expression shown in Virtual Fly Brain (VFB) + +VFB curation uses programmatic methods to generate expression statements for [FlyLight](https://www.janelia.org/project-team/flylight) hemidriver combinations. Combinations are validated against a local copy of the FlyLight dataset and loaded into FlyBase. VFB then links each expression pattern image and the curated expression information to an intersection of the two appropriate hemidrivers. + +This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemidriver transgenes. + + + + + diff --git a/content/en/docs/Concepts/templates.md b/content/en/docs/Concepts/templates.md deleted file mode 100644 index f00d3451..00000000 --- a/content/en/docs/Concepts/templates.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: "Templates" -linkTitle: "Templates" -tags: [fly brain atlas,Template,Synaptic_neuropil] -weight: 100 -description: >- - Canonical templates not only allow for spatial alignment of image data but also are often painted to make a reference atlas of anatomical regions. ---- - -Many central nervious system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB. - -## Central Nervious System from Janelia Research Campus JRC2018 - - - -VFB displays data aligned to either the [JRC 2018 unisex brain template](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFB_00101567&i=VFB_00101567) for cephalic or [JRC 2018 unisex Ventral Nerve Cord (VNC)](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00200000,VFB_00200000) for non-cephalic data. - -[Bogovic et al., "An unbiased template of the Drosophila brain and ventral nerve cord"](https://doi.org/10.1371/journal.pone.0236495) - -We recomend downloading templates from the VFB browser or the links below however the original files are available from Janelia: [JRC 2018 Brain templates](https://www.janelia.org/open-science/jrc-2018-brain-templates) - -## Adult Brain from Janelia Research Campus/VFB (JFRC2010/JFRC2) - -Superceeded by [JRC2018](https://www.virtualflybrain.org/docs/concepts/templates/#central-nervious-system-from-janelia-research-campus-jrc2018) - - - -Template brain created by Arnim Jenett (Janelia Research Campus), Kazunori Shinomiya and Kei Ito (Tokyo University) from a staining with the neuropil marker [nc82](http://www.flybase.org/reports/FBgn0259246.html). - -The voxel size is 0.62x0.62x0.62 micron. - -The files are available [here](https://github.com/VirtualFlyBrain/DrosAdultBRAINdomains). - -# Painted domains/regions in the available templates - -| Template | Painted Domains | -|----------|----------| -| [adult brain template JFRC2](http://virtualflybrain.org/reports/VFB_00017894) |[saddle](http://virtualflybrain.org/reports/VFB_00030600), [epaulette](http://virtualflybrain.org/reports/VFB_00030599), [superior posterior slope](http://virtualflybrain.org/reports/VFB_00030601), [prow](http://virtualflybrain.org/reports/VFB_00030604), [inferior posterior slope](http://virtualflybrain.org/reports/VFB_00030603), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00030605), [bulb](http://virtualflybrain.org/reports/VFB_00030625), [lobula](http://virtualflybrain.org/reports/VFB_00030622), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030623), [adult antennal lobe](http://virtualflybrain.org/reports/VFB_00030629), [wedge](http://virtualflybrain.org/reports/VFB_00030626), [anterior optic tubercle](http://virtualflybrain.org/reports/VFB_00030627), [medulla](http://virtualflybrain.org/reports/VFB_00030624), [SIP](http://virtualflybrain.org/reports/VFB_00030628), [accessory medulla](http://virtualflybrain.org/reports/VFB_00030621), [crepine](http://virtualflybrain.org/reports/VFB_00030606), [gall](http://virtualflybrain.org/reports/VFB_00030607), [anterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030608), [nodulus](http://virtualflybrain.org/reports/VFB_00030609), [gorget](http://virtualflybrain.org/reports/VFB_00030610), [ellipsoid body](http://virtualflybrain.org/reports/VFB_00030611), [lobula plate](http://virtualflybrain.org/reports/VFB_00030612), [antennal mechanosensory and motor center](http://virtualflybrain.org/reports/VFB_00030613), [inferior bridge](http://virtualflybrain.org/reports/VFB_00030631), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030630), [fan-shaped body](http://virtualflybrain.org/reports/VFB_00030633), [posterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030632), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00030614), [vest](http://virtualflybrain.org/reports/VFB_00030616), [antler](http://virtualflybrain.org/reports/VFB_00030615), [superior clamp](http://virtualflybrain.org/reports/VFB_00030618), [inferior clamp](http://virtualflybrain.org/reports/VFB_00030617), [flange](http://virtualflybrain.org/reports/VFB_00030620), [PB](http://virtualflybrain.org/reports/VFB_00030619), [cantle](http://virtualflybrain.org/reports/VFB_00030602), [posterior slope](http://virtualflybrain.org/reports/VFB_00030879), [clamp](http://virtualflybrain.org/reports/VFB_00030876), [lobula complex](http://virtualflybrain.org/reports/VFB_00030877), [adult central complex](http://virtualflybrain.org/reports/VFB_00030866), [adult mushroom body](http://virtualflybrain.org/reports/VFB_00030867), [adult cerebral ganglion](http://virtualflybrain.org/reports/VFB_00030849), [adult subesophageal zone](http://virtualflybrain.org/reports/VFB_00030856), [optic lobe](http://virtualflybrain.org/reports/VFB_00030870), [lateral horn](http://virtualflybrain.org/reports/VFB_00030900), [ventral complex](http://virtualflybrain.org/reports/VFB_00030880), [medial lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030903), [central body](http://virtualflybrain.org/reports/VFB_00030874), [lobe system of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030875), [ventrolateral neuropils](http://virtualflybrain.org/reports/VFB_00030872), [ventromedial neuropils](http://virtualflybrain.org/reports/VFB_00030873), [ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030878), [inferior neuropils](http://virtualflybrain.org/reports/VFB_00030868), [superior neuropils](http://virtualflybrain.org/reports/VFB_00030871), [adult gnathal ganglion](http://virtualflybrain.org/reports/VFB_00030840), [lateral complex](http://virtualflybrain.org/reports/VFB_00030869), [calyx of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030838), [pedunculus of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030901), [vertical lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030902) | -| [adult brain template Ito2014](http://virtualflybrain.org/reports/VFB_00030786) |[nodulus](http://virtualflybrain.org/reports/VFB_00030789), [lobula](http://virtualflybrain.org/reports/VFB_00030788), [accessory medulla](http://virtualflybrain.org/reports/VFB_00030787), [lobula plate](http://virtualflybrain.org/reports/VFB_00030807), [inferior clamp](http://virtualflybrain.org/reports/VFB_00030797), [antennal mechanosensory and motor center](http://virtualflybrain.org/reports/VFB_00030796), [cantle](http://virtualflybrain.org/reports/VFB_00030795), [bulb](http://virtualflybrain.org/reports/VFB_00030790), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030812), [superior intermediate protocerebrum](http://virtualflybrain.org/reports/VFB_00030813), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00030814), [inferior bridge](http://virtualflybrain.org/reports/VFB_00030799), [ellipsoid body](http://virtualflybrain.org/reports/VFB_00030808), [adult antennal lobe](http://virtualflybrain.org/reports/VFB_00030809), [medulla](http://virtualflybrain.org/reports/VFB_00030810), [fan-shaped body](http://virtualflybrain.org/reports/VFB_00030811), [lateral horn](http://virtualflybrain.org/reports/VFB_00030792), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00030793), [vest](http://virtualflybrain.org/reports/VFB_00030798), [protocerebral bridge](http://virtualflybrain.org/reports/VFB_00030791), [saddle](http://virtualflybrain.org/reports/VFB_00030794), [wedge commissure](http://virtualflybrain.org/reports/VFB_00030865), [superior fiber system](http://virtualflybrain.org/reports/VFB_00030862), [superior posterior lateral protocerebrum commissure](http://virtualflybrain.org/reports/VFB_00030863), [superior antennal lobe commissure](http://virtualflybrain.org/reports/VFB_00030860), [superior ellipsoid commissure](http://virtualflybrain.org/reports/VFB_00030861), [labro_frontal_nerve - painted domain, BrainName pu](http://virtualflybrain.org/reports/VFB_00030830), [lateral cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030847), [lateral equatorial fascicle](http://virtualflybrain.org/reports/VFB_00030848), [lateral accessory lobe commissure](http://virtualflybrain.org/reports/VFB_00030845), [lateral antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030846), [inferior antennal lobe commissure](http://virtualflybrain.org/reports/VFB_00030843), [inferior fiber system](http://virtualflybrain.org/reports/VFB_00030844), [pyriform fascicle](http://virtualflybrain.org/reports/VFB_00030858), [horizontal ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030842), [posterior lateral fascicle](http://virtualflybrain.org/reports/VFB_00030855), [superior AMMC commissure](http://virtualflybrain.org/reports/VFB_00030859), [mediolateral antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030853), [posterior posteriolateral protocerebral commissure](http://virtualflybrain.org/reports/VFB_00030857), [medial equatorial fascicle](http://virtualflybrain.org/reports/VFB_00030851), [posterior cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030854), [vertical ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030864), [median bundle](http://virtualflybrain.org/reports/VFB_00030852), [wedge](http://virtualflybrain.org/reports/VFB_00030817), [gorget](http://virtualflybrain.org/reports/VFB_00030820), [anterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030815), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030818), [calyx of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030821), [horizontal ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030841), [anterior optic tubercle](http://virtualflybrain.org/reports/VFB_00030819), [superior posterior slope](http://virtualflybrain.org/reports/VFB_00030822), [anterior cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030836), [antenno-subesophageal tract](http://virtualflybrain.org/reports/VFB_00030835), [anterior superior lateral protocerebrum fascicle](http://virtualflybrain.org/reports/VFB_00030839), [anterior dorsal commissure](http://virtualflybrain.org/reports/VFB_00030837), [giant fiber neuron](http://virtualflybrain.org/reports/VFB_00030832), [medial cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030850), [prow](http://virtualflybrain.org/reports/VFB_00030834), [adult gnathal ganglion](http://virtualflybrain.org/reports/VFB_00030833), [vertical lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030803), [pedunculus of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030802), [crepine](http://virtualflybrain.org/reports/VFB_00030801), [antler](http://virtualflybrain.org/reports/VFB_00030800), [superior clamp](http://virtualflybrain.org/reports/VFB_00030824), [mushroom body accessory calyx](http://virtualflybrain.org/reports/VFB_00030806), [flange](http://virtualflybrain.org/reports/VFB_00030805), [medial lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030804), [posterior optic commissure](http://virtualflybrain.org/reports/VFB_00030828), [epaulette](http://virtualflybrain.org/reports/VFB_00030825), [medial antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030826), [inferior posterior slope](http://virtualflybrain.org/reports/VFB_00030823), [posterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030816), [great commissure](http://virtualflybrain.org/reports/VFB_00030829), [adult maxillary nerve](http://virtualflybrain.org/reports/VFB_00030831), [anterior optic tract](http://virtualflybrain.org/reports/VFB_00030827) | -|[adult VNS template - Court2018](http://virtualflybrain.org/reports/VFB_00100000)|[tectulum](http://virtualflybrain.org/reports/VFB_00101131), [prothoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100016), [accessory prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100015), [cervical connective](http://virtualflybrain.org/reports/VFB_00100004), [abdominal segment 3 nerve](http://virtualflybrain.org/reports/VFB_00100008), [abdominal segment 4 nerve](http://virtualflybrain.org/reports/VFB_00100007), [posterior dorsal mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100017), [accessory metathoracic nerve](http://virtualflybrain.org/reports/VFB_00100011), [adult accessory mesothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100020), [metathoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100010), [adult metathoracic neuromere](http://virtualflybrain.org/reports/VFB_00100001), [adult mesothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100002), [dorsal prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100014), [adult prothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100003), [anterior dorsal mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100013), [abdominal nerve trunk](http://virtualflybrain.org/reports/VFB_00100006), [adult brain cell body rind](http://virtualflybrain.org/reports/VFB_00100021), [abdominal segment 2 nerve](http://virtualflybrain.org/reports/VFB_00100009), [ventral prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100022), [adult abdominal neuromere](http://virtualflybrain.org/reports/VFB_00100005), [accessory mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100018), [dorsal metathoracic nerve](http://virtualflybrain.org/reports/VFB_00100019), [mesothoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100012) | -| [L3 CNS template - Wood2018](http://virtualflybrain.org/reports/VFB_00049000)|[right dorsomedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050415), [left central subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050398), [right centromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050434), [left ventromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050511), [right central neuropil of A9](http://virtualflybrain.org/reports/VFB_00050509), [right ventral neuropil of A9](http://virtualflybrain.org/reports/VFB_00050499), [right dorsomedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050423), [lower toe](http://virtualflybrain.org/reports/VFB_00050428), [right centromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050448), [right centromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050442), [right central neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050384), [left ventral neuropil of A9](http://virtualflybrain.org/reports/VFB_00050429), [right dorsomedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050426), [left ventromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050485), [ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050397), [left ventromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050497), [left dorsomedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050372), [right central neuropil of T3](http://virtualflybrain.org/reports/VFB_00050387), [right central neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050382), [left central neuropil of A3](http://virtualflybrain.org/reports/VFB_00050407), [right T2 leg neuropil](http://virtualflybrain.org/reports/VFB_00050510), [right central neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050432), [right central neuropil of A3](http://virtualflybrain.org/reports/VFB_00050390), [right central subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050381), [left dorsomedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050374), [left central neuropil of T1](http://virtualflybrain.org/reports/VFB_00050402), [right central neuropil of A4](http://virtualflybrain.org/reports/VFB_00050391), [left central neuropil of A5](http://virtualflybrain.org/reports/VFB_00050409), [left dorsomedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050371), [right centromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050437), [right centromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050435), [right centromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050443), [right centromedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050439), [left central neuropil of A8](http://virtualflybrain.org/reports/VFB_00050412), [right dorsomedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050420), [right dorsomedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050416), [left dorsomedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050379), [right central neuropil of A6](http://virtualflybrain.org/reports/VFB_00050393), [right central neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050383), [protocerebral bridge - primordial](http://virtualflybrain.org/reports/VFB_00050396), [left central neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050399), [left dorsomedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050376), [left dorsolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050328), [left central neuropil of A4](http://virtualflybrain.org/reports/VFB_00050408), [left ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050357), [right central neuropil of A7](http://virtualflybrain.org/reports/VFB_00050394), [right central neuropil of A8](http://virtualflybrain.org/reports/VFB_00050395), [right central neuropil of A2](http://virtualflybrain.org/reports/VFB_00050389), [left dorsomedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050375), [left ventrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050361), [left ventrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050365), [left dorsomedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050377), [left central neuropil of T2](http://virtualflybrain.org/reports/VFB_00050403), [left central neuropil of A1](http://virtualflybrain.org/reports/VFB_00050405), [left central neuropil of T3](http://virtualflybrain.org/reports/VFB_00050404), [spur of mushroom body](http://virtualflybrain.org/reports/VFB_00050504), [left dorsomedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050378), [right T1 leg neuropil](http://virtualflybrain.org/reports/VFB_00050334), [left dorsomedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050368), [right dorsolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050336), [left dorsomedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050370), [left dorsomedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050369), [right dorsolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050340), [left central neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050401), [right dorsolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050337), [left T3 leg neuropil](http://virtualflybrain.org/reports/VFB_00050313), [crepine](http://virtualflybrain.org/reports/VFB_00050310), [right ventrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050307), [right ventrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050297), [right dorsolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050342), [left dorsolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050325), [left T1 leg neuropil](http://virtualflybrain.org/reports/VFB_00050330), [left dorsolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050315), [left ventrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050353), [left dorsolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050321), [right central neuropil of T1](http://virtualflybrain.org/reports/VFB_00050385), [posterior ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050331), [left ventrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050352), [left dorsomedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050373), [left dorsomedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050380), [left ventrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050359), [left ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050355), [left centromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050480), [medial lobe of mushroom body](http://virtualflybrain.org/reports/VFB_00050501), [left ventromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050486), [right dorsal neuropil of A9](http://virtualflybrain.org/reports/VFB_00050350), [right dorsolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050348), [left ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050356), [left ventrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050351), [left dorsomedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050367), [posterior inferior protocerebrum](http://virtualflybrain.org/reports/VFB_00050312), [left ventrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050360), [left dorsolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050318), [left ventrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050363), [left ventrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050354), [left dorsolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050324), [right ventrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050296), [right ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050301), [left centrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050282), [left centrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050292), [left dorsolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050326), [left dorsolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050319), [left dorsolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050316), [right ventrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050304), [nodulus - primordial](http://virtualflybrain.org/reports/VFB_00050293), [left centrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050286), [right dorsolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050338), [right dorsolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050345), [right dorsolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050343), [right dorsolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050347), [right dorsolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050335), [left ventrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050358), [left ventrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050364), [left dorsomedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050366), [left ventrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050362), [left dorsolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050320), [right ventrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050308), [right ventrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050306), [right ventrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050305), [right ventrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050303), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050329), [left dorsolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050317), [right centrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050262), [right centrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050269), [right centrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050266), [left T2 leg neuropil](http://virtualflybrain.org/reports/VFB_00050506), [left centrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050287), [left centrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050288), [right centrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050270), [fan-shaped body - primordial](http://virtualflybrain.org/reports/VFB_00050277), [right ventrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050298), [right ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050300), [left centrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050283), [left centrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050278), [left centrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050281), [left centrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050290), [right dorsolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050339), [right dorsolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050341), [right dorsolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050344), [left dorsal neuropil of A9](http://virtualflybrain.org/reports/VFB_00050349), [right dorsolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050346), [left dorsolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050327), anterior ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050332), [ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050333), [left centrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050284), [posterior superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050274), [right centrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050267), [left ventromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050494), [left centrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050289), [left dorsomedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050294), [left central neuropil of A9](http://virtualflybrain.org/reports/VFB_00050508), [superior intermediate protocerebrum](http://virtualflybrain.org/reports/VFB_00050257), [mushroom body](http://virtualflybrain.org/reports/VFB_00050505), [anterior superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050275), [right centrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050263), [right centrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050268), [right centrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050271), [right centrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050265), [left central neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050498), [pedunculus of mushroom body](http://virtualflybrain.org/reports/VFB_00050500), [right centrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050261), [right centrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050273), [right centrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050272), [right centrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050264), [left centrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050291), [left dorsolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050323), [right ventrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050295), [vertical lobe of mushroom body](http://virtualflybrain.org/reports/VFB_00050503), [left centromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050481), [left ventromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050492), [left dorsolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050322), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00050314), [right ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050299), [right ventrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050302), [right T3 leg neuropil](http://virtualflybrain.org/reports/VFB_00050311), [right ventrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050309), [right centromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050445), [calyx of mushroom body](http://virtualflybrain.org/reports/VFB_00050502), [left ventromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050483), [left ventromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050484), [left centromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050476), [left centromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050482), [left centromedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050472), [right centromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050466), [right ventromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050450), [antennal lobe](http://virtualflybrain.org/reports/VFB_00050465), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050464), [right ventromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050463), [right ventromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050461), [right ventromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050457), [left ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050487), [left ventromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050493), [left ventromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050495), [right ventromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050459), [right ventromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050460), [right ventromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050451), [right ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050455), [lateral appendix of mushroom body](http://virtualflybrain.org/reports/VFB_00050507), [left centrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050279), [left ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050489), [left ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050488), [right centrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050260), [left ventromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050490), [left centromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050479), [left centrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050285), [right dorsomedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050414), [right centromedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050440), [left central neuropil of A6](http://virtualflybrain.org/reports/VFB_00050410), [left central neuropil of A7](http://virtualflybrain.org/reports/VFB_00050411), [right dorsomedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050413), [left centromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050477), [right centromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050444), [right centromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050447), [left centromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050468), [left centromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050475), [right ventromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050449), [left centromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050478), [left centromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050469), [left centromedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050474), [clamp](http://virtualflybrain.org/reports/VFB_00050433), [right ventromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050452), [right centromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050436), [right ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050454), [right centromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050446), [right ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050453), [right ventromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050456), [left centromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050467), [right dorsomedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050421), [right dorsomedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050422), [right centromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050441), [left ventromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050491), [left ventromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050496), [right dorsomedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050258), [right ventromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050458), [right centrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050259), [left centrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050280), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050276), [left centromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050471), [right ventromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050462), [left centromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050470), [left central neuropil of A2](http://virtualflybrain.org/reports/VFB_00050406), [left central neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050400), [right dorsomedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050417), [left centromedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050473), [right ventromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050431), [right central neuropil of T2](http://virtualflybrain.org/reports/VFB_00050386), [right central neuropil of A1](http://virtualflybrain.org/reports/VFB_00050388), [right central neuropil of A5](http://virtualflybrain.org/reports/VFB_00050392), [anterior optic tubercle primordial](http://virtualflybrain.org/reports/VFB_00050430), [right centromedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050438), [right dorsomedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050424), [right dorsomedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050425), [right dorsomedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050427), [right dorsomedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050419), [right dorsomedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050418) | -| [JRC_FlyEM_Hemibrain](http://virtualflybrain.org/reports/VFB_00101384) |[PB(R3)](http://virtualflybrain.org/reports/VFB_00101491), [GOR(L)](http://virtualflybrain.org/reports/VFB_00101528), [BU(L)](http://virtualflybrain.org/reports/VFB_00101524), [LAL(L)](http://virtualflybrain.org/reports/VFB_00101526), [ATL(L)](http://virtualflybrain.org/reports/VFB_00101487), [GF(R)](http://virtualflybrain.org/reports/VFB_00101488), [PB(R1)](http://virtualflybrain.org/reports/VFB_00101489), [PB(R2)](http://virtualflybrain.org/reports/VFB_00101490), [VES(L)](http://virtualflybrain.org/reports/VFB_00101535), [NO1(R)](http://virtualflybrain.org/reports/VFB_00101543), [mALT(L)](http://virtualflybrain.org/reports/VFB_00101538), [CA(L)](http://virtualflybrain.org/reports/VFB_00101533), [PB(L6)](http://virtualflybrain.org/reports/VFB_00101503), [NO3(L)](http://virtualflybrain.org/reports/VFB_00101554), [PB(L8)](http://virtualflybrain.org/reports/VFB_00101505), [PB(L7)](http://virtualflybrain.org/reports/VFB_00101504), [SMP(L)](http://virtualflybrain.org/reports/VFB_00101507), [PB(L9)](http://virtualflybrain.org/reports/VFB_00101506), [gL(L)](http://virtualflybrain.org/reports/VFB_00101509), [SIP(L)](http://virtualflybrain.org/reports/VFB_00101508), [b\'L(L)](http://virtualflybrain.org/reports/VFB_00101511), [bL(L)](http://virtualflybrain.org/reports/VFB_00101510), [PB(R5)](http://virtualflybrain.org/reports/VFB_00101493), [CRE(L)](http://virtualflybrain.org/reports/VFB_00101512), [PB(R4)](http://virtualflybrain.org/reports/VFB_00101492), [PB(R7)](http://virtualflybrain.org/reports/VFB_00101495), [PB(R6)](http://virtualflybrain.org/reports/VFB_00101494), [PB(R8)](http://virtualflybrain.org/reports/VFB_00101496), [PB(L1)](http://virtualflybrain.org/reports/VFB_00101498), [PB(R9)](http://virtualflybrain.org/reports/VFB_00101497), [PB(L3)](http://virtualflybrain.org/reports/VFB_00101500), [PB(L2)](http://virtualflybrain.org/reports/VFB_00101499), [PB(L5)](http://virtualflybrain.org/reports/VFB_00101502), [PB(L4)](http://virtualflybrain.org/reports/VFB_00101501), [SCL(L)](http://virtualflybrain.org/reports/VFB_00101529), [SPS(L)](http://virtualflybrain.org/reports/VFB_00101532), [ICL(L)](http://virtualflybrain.org/reports/VFB_00101530), [RUB(L)](http://virtualflybrain.org/reports/VFB_00101515), [a\'L(L)](http://virtualflybrain.org/reports/VFB_00101514), [aL(L)](http://virtualflybrain.org/reports/VFB_00101513), [NO2(R)](http://virtualflybrain.org/reports/VFB_00101546), [NO3(R)](http://virtualflybrain.org/reports/VFB_00101548), [NO1(L)](http://virtualflybrain.org/reports/VFB_00101550), [NO2(L)](http://virtualflybrain.org/reports/VFB_00101553), [AL(L)](http://virtualflybrain.org/reports/VFB_00101484), [AOT(R)](http://virtualflybrain.org/reports/VFB_00101483), [GA(R)](http://virtualflybrain.org/reports/VFB_00101486), [POC](http://virtualflybrain.org/reports/VFB_00101485), [IPS(R)](http://virtualflybrain.org/reports/VFB_00101455), [SAD](http://virtualflybrain.org/reports/VFB_00101456), [GC](http://virtualflybrain.org/reports/VFB_00101478), [mALT(R)](http://virtualflybrain.org/reports/VFB_00101477), [AL(R)](http://virtualflybrain.org/reports/VFB_00101449), [VES(R)](http://virtualflybrain.org/reports/VFB_00101450), [SPS(R)](http://virtualflybrain.org/reports/VFB_00101454), [ATL(R)](http://virtualflybrain.org/reports/VFB_00101445), [IB](http://virtualflybrain.org/reports/VFB_00101443), [ICL(R)](http://virtualflybrain.org/reports/VFB_00101442), [GOR(R)](http://virtualflybrain.org/reports/VFB_00101453), [EPA(R)](http://virtualflybrain.org/reports/VFB_00101451), [CAN(R)](http://virtualflybrain.org/reports/VFB_00101459), [PRW](http://virtualflybrain.org/reports/VFB_00101460), [FLA(R)](http://virtualflybrain.org/reports/VFB_00101458), [GNG](http://virtualflybrain.org/reports/VFB_00101468), [CA(R)](http://virtualflybrain.org/reports/VFB_00101389), [LOP(R)](http://virtualflybrain.org/reports/VFB_00101388), [PED(R)](http://virtualflybrain.org/reports/VFB_00101390), [AMMC](http://virtualflybrain.org/reports/VFB_00101457), [b\'L(R)](http://virtualflybrain.org/reports/VFB_00101396), [LO(R)](http://virtualflybrain.org/reports/VFB_00101387), [ME(R)](http://virtualflybrain.org/reports/VFB_00101385), [AME(R)](http://virtualflybrain.org/reports/VFB_00101386), [a\'L(R)](http://virtualflybrain.org/reports/VFB_00101393), [aL(R)](http://virtualflybrain.org/reports/VFB_00101391), [bL(R)](http://virtualflybrain.org/reports/VFB_00101395), [RUB(R)](http://virtualflybrain.org/reports/VFB_00101440), [SCL(R)](http://virtualflybrain.org/reports/VFB_00101441), [SMP(R)](http://virtualflybrain.org/reports/VFB_00101437), [CRE(R)](http://virtualflybrain.org/reports/VFB_00101438), [ROB(R)](http://virtualflybrain.org/reports/VFB_00101439), [WED(R)](http://virtualflybrain.org/reports/VFB_00101419), [SLP(R)](http://virtualflybrain.org/reports/VFB_00101435), [LH(R)](http://virtualflybrain.org/reports/VFB_00101434), [SIP(R)](http://virtualflybrain.org/reports/VFB_00101436), [PVLP(R)](http://virtualflybrain.org/reports/VFB_00101416), [AVLP(R)](http://virtualflybrain.org/reports/VFB_00101408), [PLP(R)](http://virtualflybrain.org/reports/VFB_00101417), [AOTU(R)](http://virtualflybrain.org/reports/VFB_00101407), [PB](http://virtualflybrain.org/reports/VFB_00101401), [LAL(R)](http://virtualflybrain.org/reports/VFB_00101403), [FB](http://virtualflybrain.org/reports/VFB_00101398), [BU(R)](http://virtualflybrain.org/reports/VFB_00101402), [EB](http://virtualflybrain.org/reports/VFB_00101400), [gL(R)](http://virtualflybrain.org/reports/VFB_00101397), [AB(R)](http://virtualflybrain.org/reports/VFB_00101399), [AB(L)](http://virtualflybrain.org/reports/VFB_00102288), [EPA(L)](http://virtualflybrain.org/reports/VFB_00102287) | -| [JRC2018Unisex](http://virtualflybrain.org/reports/VFB_00101567) |[ICL](http://virtualflybrain.org/reports/VFB_00102179), [ROB](http://virtualflybrain.org/reports/VFB_00102174), [GOR](http://virtualflybrain.org/reports/VFB_00102214), [SLP](http://virtualflybrain.org/reports/VFB_00102162), [RUB](http://virtualflybrain.org/reports/VFB_00102175), [CRE](http://virtualflybrain.org/reports/VFB_00102171), [SMP](http://virtualflybrain.org/reports/VFB_00102170), [SPS](http://virtualflybrain.org/reports/VFB_00102215), [CAN](http://virtualflybrain.org/reports/VFB_00102275), [SCL](http://virtualflybrain.org/reports/VFB_00102176), [SIP](http://virtualflybrain.org/reports/VFB_00102164), [IB](http://virtualflybrain.org/reports/VFB_00102185), [ATL](http://virtualflybrain.org/reports/VFB_00102190), [AL](http://virtualflybrain.org/reports/VFB_00102201), [EPA](http://virtualflybrain.org/reports/VFB_00102213), [VES](http://virtualflybrain.org/reports/VFB_00102212), [LH](http://virtualflybrain.org/reports/VFB_00102159), [LO](http://virtualflybrain.org/reports/VFB_00102109), [SAD](http://virtualflybrain.org/reports/VFB_00102271), [AME](http://virtualflybrain.org/reports/VFB_00102108), [PVLP](http://virtualflybrain.org/reports/VFB_00102148), [AVLP](http://virtualflybrain.org/reports/VFB_00102146), [WED](http://virtualflybrain.org/reports/VFB_00102154), [PRW](http://virtualflybrain.org/reports/VFB_00102276), [AMMC](http://virtualflybrain.org/reports/VFB_00102273), [aL](http://virtualflybrain.org/reports/VFB_00102119), [LOP](http://virtualflybrain.org/reports/VFB_00102110), [a\'L](http://virtualflybrain.org/reports/VFB_00102121), [bL](http://virtualflybrain.org/reports/VFB_00102123), [ME](http://virtualflybrain.org/reports/VFB_00102107), [PED](http://virtualflybrain.org/reports/VFB_00102118), [CA](http://virtualflybrain.org/reports/VFB_00102114), [NO](http://virtualflybrain.org/reports/VFB_00102282), [GA](http://virtualflybrain.org/reports/VFB_00102281), [AOTU](http://virtualflybrain.org/reports/VFB_00102141), [BU](http://virtualflybrain.org/reports/VFB_00102139), [PLP](http://virtualflybrain.org/reports/VFB_00102152), [GNG](http://virtualflybrain.org/reports/VFB_00102280), [EB](http://virtualflybrain.org/reports/VFB_00102135), [LAL](http://virtualflybrain.org/reports/VFB_00102140), [PB](http://virtualflybrain.org/reports/VFB_00102137), [IPS](http://virtualflybrain.org/reports/VFB_00102218), [b\'L](http://virtualflybrain.org/reports/VFB_00102124), [gL](http://virtualflybrain.org/reports/VFB_00102133), [FB](http://virtualflybrain.org/reports/VFB_00102134), [FLA](http://virtualflybrain.org/reports/VFB_00102274) | - diff --git a/content/en/docs/Concepts/transgene.md b/content/en/docs/Concepts/transgene.md index 0cf531ca..6a06753e 100644 --- a/content/en/docs/Concepts/transgene.md +++ b/content/en/docs/Concepts/transgene.md @@ -1,16 +1,14 @@ --- -title: "Transgene Expression" -linkTitle: "Transgene Expression" +title: "Curation of Transgene Expression in VFB" +linkTitle: "Transgene Expression Curation" categories: ["overview","help"] tags: ["Expression_pattern","transgene","FlyLight"] weight: 20 description: > - These techniques work by driving the expression of a target transgenes. + Details of the curation procedure for transgene expression patterns. --- -Here we present details of how single transgenes are curated - Transgene expression into FlyBase and Virtual Fly Brain (VFB) -Expression of single transgenes are curated from the published literature into [FlyBase](http://flybase.org) as expression statements. [Virtual Fly Brain (VFB)](https://virtualflybrain.org) combines hosted images with neuroanatomical, expression and genetic data from [FlyBase](https://flybase.org/) in Neo4j and maps them onto [Central Nervious System (CNS)](https://www.virtualflybrain.org/term/central-nervous-system-fbbt_00005094/) [templates](/tags/template/) where they can be queried using [Web Ontology Language (OWL)](https://www.w3.org/OWL/) and [Solr](https://solr.apache.org/). +Virtual Fly Brain (VFB) and FlyBase curators record information from the literature about the expression of single transgenes using ontology terms and load this into FlyBase. VFB combines curated expression, genetic and publication data from FlyBase with 3D images of the expression patterns aligned to standard [templates](/docs/data/templates/). These annotated images can then be searched and queried via the [web interface](/docs/website-features/search_query/) or [APIs](/docs/apis/). diff --git a/content/en/docs/Contribution guidelines/_index.md b/content/en/docs/Contribution guidelines/_index.md index 64b22ce5..d9f347df 100644 --- a/content/en/docs/Contribution guidelines/_index.md +++ b/content/en/docs/Contribution guidelines/_index.md @@ -1,10 +1,10 @@ --- title: "Contribution Guidelines" linkTitle: "Contribution Guidelines" -weight: 10 +weight: 20 categories: ["help"] description: > - Contribute or update Virtual Fly Brain data/sites + Contribute or update Virtual Fly Brain data/sites. --- Submitting new data to VFB diff --git a/content/en/docs/Data/EM/_index.md b/content/en/docs/Data/EM/_index.md new file mode 100644 index 00000000..5da47cbc --- /dev/null +++ b/content/en/docs/Data/EM/_index.md @@ -0,0 +1,29 @@ +--- +title: "Electron Microscopy Data" +linkTitle: "EM Data" +weight: 1 +description: > + Electron Microscopy Data available on Virtual Fly Brain. + +--- + +Virtual Fly Brain brings together data from multiple [electron microscopy (EM) resources](/docs/resources/), providing access to high-resolution neuroanatomical datasets. These datasets include complete EM volumes of Drosophila brains and ventral nerve cords, neuron reconstructions, connectivity information and neurotransmitter predictions. Data can be visualised using the web browser or accessed programmatically via [APIs](/docs/apis/). + +## Comparison Table of Integrated Datasets + +The table below summarises EM datasets that have been integrated into VFB, including the portion of the organism covered (`Anatomy`), the resource(s) where the original data can be found, The level of reconstruction (sparse or dense) and the original publication for the dataset. + +| Dataset | VFB symbol | Anatomy | Reconstruction | Resource(s) | Original Publication | +|------|------------|------------------------------|----------------|-------|----------------------------------------------------------------------------------------------------------------------------------------------| +| BANC | BANC | Full CNS (adult female) | Dense | Codex | [Bates et al. (2025)](https://doi.org/10.1101/2025.07.31.667571) | +| Optic-lobe | ol | Optic lobe (adult male) | Dense | NeuPrint; Codex | [Nern et al. (2025)](https://doi.org/10.1038/s41586-025-08746-0) | +| FAFB (FlyWire) | fw | Full brain (female larva) | Dense | Codex | [Dorkenwald et al. (2024)](https://doi.org/10.1038/s41586-024-07558-y); [Schlegel et al. (2024)](https://doi.org/10.1038/s41586-024-07686-5) | +| MANC | mv | Full VNC (adult male) | Dense | NeuPrint; Codex | [Takemura et al. (2024)](https://doi.org/10.7554/eLife.97769.1) | +| FANC | N/A | Full VNS (adult female) | Sparse | CATMAID | [Phelps et al. (2021)](https://doi.org/10.1016/j.cell.2020.12.013) | +| Hemibrain | hb | Partial brain (adult female) | Dense | NeuPrint | [Scheffer et al. (2020)](https://doi.org/10.7554/eLife.57443) +| FAFB (CATMAID) | fafb | Full brain (adult female) | Sparse | CATMAID | [Zheng et al. (2018)](https://doi.org/10.1016/j.cell.2018.06.019) | +| l1em | l1em | Full CNS (female larva) | Sparse | CATMAID | [Ohyama et al. (2015)](https://doi.org/10.1038/nature14297) | + +## Datasets Hosted by VFB + +Virtual Fly Brain (VFB) hosts several CATMAID instances for exploring connectomic reconstruction data. These datasets provide access to neuroanatomical data from various Drosophila electron microscopy projects. Full details are available [here](/hosted/). \ No newline at end of file diff --git a/content/en/docs/Data/LM/_index.md b/content/en/docs/Data/LM/_index.md new file mode 100644 index 00000000..1261956a --- /dev/null +++ b/content/en/docs/Data/LM/_index.md @@ -0,0 +1,11 @@ +--- +title: "Light Microscopy Data" +linkTitle: "LM Data" +weight: 5 +description: > + Light Microscopy Data available on Virtual Fly Brain. + +--- + +Virtual Fly Brain brings together data from multiple [Light Microscopy (LM) resources](/docs/resources/), providing access to visualisations of driver (including split) expression patterns. + diff --git a/content/en/docs/Data/LM/flylight/index.md b/content/en/docs/Data/LM/flylight/index.md new file mode 100644 index 00000000..e8a71a37 --- /dev/null +++ b/content/en/docs/Data/LM/flylight/index.md @@ -0,0 +1,32 @@ +--- +title: "Janelia FlyLight" +linkTitle: "FlyLight" +weight: 20 +tags: ["Split","Expression_pattern","transgene","FlyLight","Janelia","Larval","MCFO","NeuronBridge"] +description: > + The FlyLight Project produces large anatomical data sets and highly characterized collections of GAL4, LexA and Split-GAL4 drivers in order to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system. +cascade: +- type: "docs" + _target: + path: "/**" +--- + +## Introduction + +FlyLight makes its primary data available via VFB as well as through dedicated websites for expression patterns of Generation 1 GAL4 and LexA lines and for split-GAL4 lines. Generation 1, split hemidriver, and stable split combination lines are available primarily from the [Bloomington Stock Center](https://bdsc.indiana.edu/). Stable split lines can also be requested via the split-GAL4 website. + +## FlyLight Data and Resources + +FlyLight data is integrated and indexed on [VFB](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=VFB_00101567,AllDatasets) and direct linkouts are provided from the [Term Info tabs](/docs/website-features/terminfo/#references-and-linkouts) to the original images. VFB hosts the original larval images [here](https://raw.larval.flylight.virtualflybrain.org/). External links to the original collections of adult images are provided below: + +[Generation 1 GAL4 expression patterns](https://flweb.janelia.org/) + +[Generation 1 MCFO (single neuron) patterns](https://gen1mcfo.janelia.org/) + +[Split-GAL4 Expression Patterns](https://splitgal4.janelia.org/) + +[Janelia Raw Image Collection](https://flylight-raw.janelia.org/cgi-bin/raw.cgi) + +Light and EM neurons can also be searched for on [NeuronBridge](https://neuronbridge.janelia.org/) + +Also see [FlyLight Imaging Tile Documentation](/docs/concepts/flylight_tiles/). \ No newline at end of file diff --git a/content/en/docs/Data/_index.md b/content/en/docs/Data/_index.md new file mode 100755 index 00000000..ca6f5528 --- /dev/null +++ b/content/en/docs/Data/_index.md @@ -0,0 +1,14 @@ +--- +title: "Data on VFB" +linkTitle: "Data" +weight: 9 +date: 2026-01-19 +description: > + Types of data and datasets that are available on Virtual Fly Brain. +cascade: +- type: "docs" + _target: + path: "/**" +--- + +VFB hosts a range of datatypes, including electron microscopy (EM) and light microscopy (LM) datasets with images annotated using the same cell type ontology terms and aligned to common standard templates. We also host single cell RNA sequencing (scRNAseq) gene expression data. diff --git a/content/en/docs/Data/scRNAseq/_index.md b/content/en/docs/Data/scRNAseq/_index.md new file mode 100644 index 00000000..09eca70f --- /dev/null +++ b/content/en/docs/Data/scRNAseq/_index.md @@ -0,0 +1,24 @@ +--- +title: "Single Cell RNA Sequencing Data" +linkTitle: "scRNAseq Data" +weight: 15 +description: > + scRNAseq Data available on Virtual Fly Brain. + +--- + +Virtual Fly Brain incorporates scRNAseq data from multiple studies, including the [Fly Cell Atlas](https://flycellatlas.org/), [Aging Fly Cell Atlas](https://hongjielilab.org/afca/) and other datasets that identify nervous system cell types - full list [here](https://github.com/VirtualFlyBrain/VFB_reporting_results/blob/master/scRNAseq_DataSets.tsv). These datasets can be found by searching for 'scRNAseq' and filtering to 'Dataset'. + +Clusters can be found for particular cell types via the `Single cell transcriptomics data for..` query on the cell type Term Info pane. + +![transcriptomics_query](https://www.virtualflybrain.org/images/scRNAseq/cluster_query.png) + +Genes for a particular cluster can be filtered by function and sorted by expression level and extent (proportion of cells in cluster expressing the gene). As with other VFB search results, these can be exported as a csv. + +_Note that we currently only include genes that have extent > 0.2 in a cluster._ + +![cluster_genes](https://www.virtualflybrain.org/images/scRNAseq/gene_expression.png) + +Data can also be retrieved using [VFB_connect](https://vfb-connect.readthedocs.io/en/stable/API_reference.html#transcriptomics-queries). + +We pull scRNAseq data from [FlyBase](https://flybase.org/), which takes it from the [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home). diff --git a/content/en/docs/Data/templates.md b/content/en/docs/Data/templates.md new file mode 100644 index 00000000..2cb5147a --- /dev/null +++ b/content/en/docs/Data/templates.md @@ -0,0 +1,42 @@ +--- +title: "Templates" +linkTitle: "Templates" +tags: [fly brain atlas,Template,Synaptic_neuropil] +weight: 100 +description: >- + Summary of templates on Virtual Fly Brain and the painted domains/regions available in those templates. +--- + +Canonical templates not only allow for spatial alignment of image data, but also are often painted to make a reference atlas of anatomical regions. Many central nervous system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB. Templates can be downloaded from their [Term Info](/docs/website-features/terminfo/#data) pages. + +## Central Nervous System from Janelia Research Campus JRC2018 + + + +VFB displays data aligned to the [JRC 2018 unisex brain template](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFB_00101567&i=VFB_00101567) or [JRC 2018 unisex Ventral Nerve Cord (VNC)](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00200000,VFB_00200000), as appropriate. See [Bogovic et al., "An unbiased template of the Drosophila brain and ventral nerve cord"](https://doi.org/10.1371/journal.pone.0236495) for details of template generation. + +The original files are available from Janelia: [JRC 2018 Brain templates](https://www.janelia.org/open-science/jrc-2018-brain-templates). + +## Adult Brain from Janelia Research Campus/VFB (JFRC2010/JFRC2) + +Superceeded by [JRC2018](#central-nervous-system-from-janelia-research-campus-jrc2018) + + + +Template brain created by Arnim Jenett (Janelia Research Campus), Kazunori Shinomiya and Kei Ito (Tokyo University) from a staining with the neuropil marker [nc82](http://www.flybase.org/reports/FBgn0259246.html). + +The voxel size is 0.62x0.62x0.62 microns. + +The files are available [here](https://github.com/VirtualFlyBrain/DrosAdultBRAINdomains). + +# Painted domains/regions in the available templates + +| Template | Painted Domains | +|----------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| [adult brain template JFRC2](http://virtualflybrain.org/reports/VFB_00017894) | [saddle](http://virtualflybrain.org/reports/VFB_00030600), [epaulette](http://virtualflybrain.org/reports/VFB_00030599), [superior posterior slope](http://virtualflybrain.org/reports/VFB_00030601), [prow](http://virtualflybrain.org/reports/VFB_00030604), [inferior posterior slope](http://virtualflybrain.org/reports/VFB_00030603), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00030605), [bulb](http://virtualflybrain.org/reports/VFB_00030625), [lobula](http://virtualflybrain.org/reports/VFB_00030622), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030623), [adult antennal lobe](http://virtualflybrain.org/reports/VFB_00030629), [wedge](http://virtualflybrain.org/reports/VFB_00030626), [anterior optic tubercle](http://virtualflybrain.org/reports/VFB_00030627), [medulla](http://virtualflybrain.org/reports/VFB_00030624), [SIP](http://virtualflybrain.org/reports/VFB_00030628), [accessory medulla](http://virtualflybrain.org/reports/VFB_00030621), [crepine](http://virtualflybrain.org/reports/VFB_00030606), [gall](http://virtualflybrain.org/reports/VFB_00030607), [anterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030608), [nodulus](http://virtualflybrain.org/reports/VFB_00030609), [gorget](http://virtualflybrain.org/reports/VFB_00030610), [ellipsoid body](http://virtualflybrain.org/reports/VFB_00030611), [lobula plate](http://virtualflybrain.org/reports/VFB_00030612), [antennal mechanosensory and motor center](http://virtualflybrain.org/reports/VFB_00030613), [inferior bridge](http://virtualflybrain.org/reports/VFB_00030631), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030630), [fan-shaped body](http://virtualflybrain.org/reports/VFB_00030633), [posterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030632), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00030614), [vest](http://virtualflybrain.org/reports/VFB_00030616), [antler](http://virtualflybrain.org/reports/VFB_00030615), [superior clamp](http://virtualflybrain.org/reports/VFB_00030618), [inferior clamp](http://virtualflybrain.org/reports/VFB_00030617), [flange](http://virtualflybrain.org/reports/VFB_00030620), [PB](http://virtualflybrain.org/reports/VFB_00030619), [cantle](http://virtualflybrain.org/reports/VFB_00030602), [posterior slope](http://virtualflybrain.org/reports/VFB_00030879), [clamp](http://virtualflybrain.org/reports/VFB_00030876), [lobula complex](http://virtualflybrain.org/reports/VFB_00030877), [adult central complex](http://virtualflybrain.org/reports/VFB_00030866), [adult mushroom body](http://virtualflybrain.org/reports/VFB_00030867), [adult cerebral ganglion](http://virtualflybrain.org/reports/VFB_00030849), [adult subesophageal zone](http://virtualflybrain.org/reports/VFB_00030856), [optic lobe](http://virtualflybrain.org/reports/VFB_00030870), [lateral horn](http://virtualflybrain.org/reports/VFB_00030900), [ventral complex](http://virtualflybrain.org/reports/VFB_00030880), [medial lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030903), [central body](http://virtualflybrain.org/reports/VFB_00030874), [lobe system of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030875), [ventrolateral neuropils](http://virtualflybrain.org/reports/VFB_00030872), [ventromedial neuropils](http://virtualflybrain.org/reports/VFB_00030873), [ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030878), [inferior neuropils](http://virtualflybrain.org/reports/VFB_00030868), [superior neuropils](http://virtualflybrain.org/reports/VFB_00030871), [adult gnathal ganglion](http://virtualflybrain.org/reports/VFB_00030840), [lateral complex](http://virtualflybrain.org/reports/VFB_00030869), [calyx of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030838), [pedunculus of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030901), [vertical lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030902) | +| [adult brain template Ito2014](http://virtualflybrain.org/reports/VFB_00030786) | [nodulus](http://virtualflybrain.org/reports/VFB_00030789), [lobula](http://virtualflybrain.org/reports/VFB_00030788), [accessory medulla](http://virtualflybrain.org/reports/VFB_00030787), [lobula plate](http://virtualflybrain.org/reports/VFB_00030807), [inferior clamp](http://virtualflybrain.org/reports/VFB_00030797), [antennal mechanosensory and motor center](http://virtualflybrain.org/reports/VFB_00030796), [cantle](http://virtualflybrain.org/reports/VFB_00030795), [bulb](http://virtualflybrain.org/reports/VFB_00030790), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030812), [superior intermediate protocerebrum](http://virtualflybrain.org/reports/VFB_00030813), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00030814), [inferior bridge](http://virtualflybrain.org/reports/VFB_00030799), [ellipsoid body](http://virtualflybrain.org/reports/VFB_00030808), [adult antennal lobe](http://virtualflybrain.org/reports/VFB_00030809), [medulla](http://virtualflybrain.org/reports/VFB_00030810), [fan-shaped body](http://virtualflybrain.org/reports/VFB_00030811), [lateral horn](http://virtualflybrain.org/reports/VFB_00030792), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00030793), [vest](http://virtualflybrain.org/reports/VFB_00030798), [protocerebral bridge](http://virtualflybrain.org/reports/VFB_00030791), [saddle](http://virtualflybrain.org/reports/VFB_00030794), [wedge commissure](http://virtualflybrain.org/reports/VFB_00030865), [superior fiber system](http://virtualflybrain.org/reports/VFB_00030862), [superior posterior lateral protocerebrum commissure](http://virtualflybrain.org/reports/VFB_00030863), [superior antennal lobe commissure](http://virtualflybrain.org/reports/VFB_00030860), [superior ellipsoid commissure](http://virtualflybrain.org/reports/VFB_00030861), [labro_frontal_nerve - painted domain, BrainName pu](http://virtualflybrain.org/reports/VFB_00030830), [lateral cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030847), [lateral equatorial fascicle](http://virtualflybrain.org/reports/VFB_00030848), [lateral accessory lobe commissure](http://virtualflybrain.org/reports/VFB_00030845), [lateral antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030846), [inferior antennal lobe commissure](http://virtualflybrain.org/reports/VFB_00030843), [inferior fiber system](http://virtualflybrain.org/reports/VFB_00030844), [pyriform fascicle](http://virtualflybrain.org/reports/VFB_00030858), [horizontal ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030842), [posterior lateral fascicle](http://virtualflybrain.org/reports/VFB_00030855), [superior AMMC commissure](http://virtualflybrain.org/reports/VFB_00030859), [mediolateral antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030853), [posterior posteriolateral protocerebral commissure](http://virtualflybrain.org/reports/VFB_00030857), [medial equatorial fascicle](http://virtualflybrain.org/reports/VFB_00030851), [posterior cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030854), [vertical ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030864), [median bundle](http://virtualflybrain.org/reports/VFB_00030852), [wedge](http://virtualflybrain.org/reports/VFB_00030817), [gorget](http://virtualflybrain.org/reports/VFB_00030820), [anterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030815), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030818), [calyx of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030821), [horizontal ventrolateral protocerebral fascicle](http://virtualflybrain.org/reports/VFB_00030841), [anterior optic tubercle](http://virtualflybrain.org/reports/VFB_00030819), [superior posterior slope](http://virtualflybrain.org/reports/VFB_00030822), [anterior cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030836), [antenno-subesophageal tract](http://virtualflybrain.org/reports/VFB_00030835), [anterior superior lateral protocerebrum fascicle](http://virtualflybrain.org/reports/VFB_00030839), [anterior dorsal commissure](http://virtualflybrain.org/reports/VFB_00030837), [giant fiber neuron](http://virtualflybrain.org/reports/VFB_00030832), [medial cerebro-cervical fascicle](http://virtualflybrain.org/reports/VFB_00030850), [prow](http://virtualflybrain.org/reports/VFB_00030834), [adult gnathal ganglion](http://virtualflybrain.org/reports/VFB_00030833), [vertical lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030803), [pedunculus of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030802), [crepine](http://virtualflybrain.org/reports/VFB_00030801), [antler](http://virtualflybrain.org/reports/VFB_00030800), [superior clamp](http://virtualflybrain.org/reports/VFB_00030824), [mushroom body accessory calyx](http://virtualflybrain.org/reports/VFB_00030806), [flange](http://virtualflybrain.org/reports/VFB_00030805), [medial lobe of adult mushroom body](http://virtualflybrain.org/reports/VFB_00030804), [posterior optic commissure](http://virtualflybrain.org/reports/VFB_00030828), [epaulette](http://virtualflybrain.org/reports/VFB_00030825), [medial antennal lobe tract](http://virtualflybrain.org/reports/VFB_00030826), [inferior posterior slope](http://virtualflybrain.org/reports/VFB_00030823), [posterior ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00030816), [great commissure](http://virtualflybrain.org/reports/VFB_00030829), [adult maxillary nerve](http://virtualflybrain.org/reports/VFB_00030831), [anterior optic tract](http://virtualflybrain.org/reports/VFB_00030827) | +|[adult VNS template - Court2018](http://virtualflybrain.org/reports/VFB_00100000)| [tectulum](http://virtualflybrain.org/reports/VFB_00101131), [prothoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100016), [accessory prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100015), [cervical connective](http://virtualflybrain.org/reports/VFB_00100004), [abdominal segment 3 nerve](http://virtualflybrain.org/reports/VFB_00100008), [abdominal segment 4 nerve](http://virtualflybrain.org/reports/VFB_00100007), [posterior dorsal mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100017), [accessory metathoracic nerve](http://virtualflybrain.org/reports/VFB_00100011), [adult accessory mesothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100020), [metathoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100010), [adult metathoracic neuromere](http://virtualflybrain.org/reports/VFB_00100001), [adult mesothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100002), [dorsal prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100014), [adult prothoracic neuromere](http://virtualflybrain.org/reports/VFB_00100003), [anterior dorsal mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100013), [abdominal nerve trunk](http://virtualflybrain.org/reports/VFB_00100006), [adult brain cell body rind](http://virtualflybrain.org/reports/VFB_00100021), [abdominal segment 2 nerve](http://virtualflybrain.org/reports/VFB_00100009), [ventral prothoracic nerve](http://virtualflybrain.org/reports/VFB_00100022), [adult abdominal neuromere](http://virtualflybrain.org/reports/VFB_00100005), [accessory mesothoracic nerve](http://virtualflybrain.org/reports/VFB_00100018), [dorsal metathoracic nerve](http://virtualflybrain.org/reports/VFB_00100019), [mesothoracic leg nerve](http://virtualflybrain.org/reports/VFB_00100012) | +| [L3 CNS template - Wood2018](http://virtualflybrain.org/reports/VFB_00049000)| [right dorsomedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050415), [left central subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050398), [right centromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050434), [left ventromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050511), [right central neuropil of A9](http://virtualflybrain.org/reports/VFB_00050509), [right ventral neuropil of A9](http://virtualflybrain.org/reports/VFB_00050499), [right dorsomedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050423), [lower toe](http://virtualflybrain.org/reports/VFB_00050428), [right centromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050448), [right centromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050442), [right central neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050384), [left ventral neuropil of A9](http://virtualflybrain.org/reports/VFB_00050429), [right dorsomedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050426), [left ventromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050485), [ventrolateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050397), [left ventromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050497), [left dorsomedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050372), [right central neuropil of T3](http://virtualflybrain.org/reports/VFB_00050387), [right central neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050382), [left central neuropil of A3](http://virtualflybrain.org/reports/VFB_00050407), [right T2 leg neuropil](http://virtualflybrain.org/reports/VFB_00050510), [right central neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050432), [right central neuropil of A3](http://virtualflybrain.org/reports/VFB_00050390), [right central subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050381), [left dorsomedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050374), [left central neuropil of T1](http://virtualflybrain.org/reports/VFB_00050402), [right central neuropil of A4](http://virtualflybrain.org/reports/VFB_00050391), [left central neuropil of A5](http://virtualflybrain.org/reports/VFB_00050409), [left dorsomedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050371), [right centromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050437), [right centromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050435), [right centromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050443), [right centromedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050439), [left central neuropil of A8](http://virtualflybrain.org/reports/VFB_00050412), [right dorsomedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050420), [right dorsomedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050416), [left dorsomedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050379), [right central neuropil of A6](http://virtualflybrain.org/reports/VFB_00050393), [right central neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050383), [protocerebral bridge - primordial](http://virtualflybrain.org/reports/VFB_00050396), [left central neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050399), [left dorsomedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050376), [left dorsolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050328), [left central neuropil of A4](http://virtualflybrain.org/reports/VFB_00050408), [left ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050357), [right central neuropil of A7](http://virtualflybrain.org/reports/VFB_00050394), [right central neuropil of A8](http://virtualflybrain.org/reports/VFB_00050395), [right central neuropil of A2](http://virtualflybrain.org/reports/VFB_00050389), [left dorsomedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050375), [left ventrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050361), [left ventrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050365), [left dorsomedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050377), [left central neuropil of T2](http://virtualflybrain.org/reports/VFB_00050403), [left central neuropil of A1](http://virtualflybrain.org/reports/VFB_00050405), [left central neuropil of T3](http://virtualflybrain.org/reports/VFB_00050404), [spur of mushroom body](http://virtualflybrain.org/reports/VFB_00050504), [left dorsomedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050378), [right T1 leg neuropil](http://virtualflybrain.org/reports/VFB_00050334), [left dorsomedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050368), [right dorsolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050336), [left dorsomedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050370), [left dorsomedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050369), [right dorsolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050340), [left central neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050401), [right dorsolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050337), [left T3 leg neuropil](http://virtualflybrain.org/reports/VFB_00050313), [crepine](http://virtualflybrain.org/reports/VFB_00050310), [right ventrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050307), [right ventrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050297), [right dorsolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050342), [left dorsolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050325), [left T1 leg neuropil](http://virtualflybrain.org/reports/VFB_00050330), [left dorsolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050315), [left ventrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050353), [left dorsolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050321), [right central neuropil of T1](http://virtualflybrain.org/reports/VFB_00050385), [posterior ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050331), [left ventrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050352), [left dorsomedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050373), [left dorsomedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050380), [left ventrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050359), [left ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050355), [left centromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050480), [medial lobe of mushroom body](http://virtualflybrain.org/reports/VFB_00050501), [left ventromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050486), [right dorsal neuropil of A9](http://virtualflybrain.org/reports/VFB_00050350), [right dorsolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050348), [left ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050356), [left ventrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050351), [left dorsomedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050367), [posterior inferior protocerebrum](http://virtualflybrain.org/reports/VFB_00050312), [left ventrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050360), [left dorsolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050318), [left ventrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050363), [left ventrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050354), [left dorsolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050324), [right ventrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050296), [right ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050301), [left centrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050282), [left centrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050292), [left dorsolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050326), [left dorsolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050319), [left dorsolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050316), [right ventrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050304), [nodulus - primordial](http://virtualflybrain.org/reports/VFB_00050293), [left centrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050286), [right dorsolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050338), [right dorsolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050345), [right dorsolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050343), [right dorsolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050347), [right dorsolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050335), [left ventrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050358), [left ventrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050364), [left dorsomedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050366), [left ventrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050362), [left dorsolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050320), [right ventrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050308), [right ventrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050306), [right ventrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050305), [right ventrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050303), [posterior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050329), [left dorsolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050317), [right centrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050262), [right centrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050269), [right centrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050266), [left T2 leg neuropil](http://virtualflybrain.org/reports/VFB_00050506), [left centrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050287), [left centrolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050288), [right centrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050270), [fan-shaped body - primordial](http://virtualflybrain.org/reports/VFB_00050277), [right ventrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050298), [right ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050300), [left centrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050283), [left centrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050278), [left centrolateral neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050281), [left centrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050290), [right dorsolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050339), [right dorsolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050341), [right dorsolateral neuropil of A4](http://virtualflybrain.org/reports/VFB_00050344), [left dorsal neuropil of A9](http://virtualflybrain.org/reports/VFB_00050349), [right dorsolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050346), [left dorsolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050327), [anterior ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050332), [ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050333), [left centrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050284), [posterior superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050274), [right centrolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050267), [left ventromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050494), [left centrolateral neuropil of A5](http://virtualflybrain.org/reports/VFB_00050289), [left dorsomedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050294), [left central neuropil of A9](http://virtualflybrain.org/reports/VFB_00050508), [superior intermediate protocerebrum](http://virtualflybrain.org/reports/VFB_00050257), [mushroom body](http://virtualflybrain.org/reports/VFB_00050505), [anterior superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050275), [right centrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050263), [right centrolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050268), [right centrolateral neuropil of A6](http://virtualflybrain.org/reports/VFB_00050271), [right centrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050265), [left central neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050498), [pedunculus of mushroom body](http://virtualflybrain.org/reports/VFB_00050500), [right centrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050261), [right centrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050273), [right centrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050272), [right centrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050264), [left centrolateral neuropil of A7](http://virtualflybrain.org/reports/VFB_00050291), [left dorsolateral neuropil of A3](http://virtualflybrain.org/reports/VFB_00050323), [right ventrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050295), [vertical lobe of mushroom body](http://virtualflybrain.org/reports/VFB_00050503), [left centromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050481), [left ventromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050492), [left dorsolateral neuropil of A2](http://virtualflybrain.org/reports/VFB_00050322), [lateral accessory lobe](http://virtualflybrain.org/reports/VFB_00050314), [right ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050299), [right ventrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050302), [right T3 leg neuropil](http://virtualflybrain.org/reports/VFB_00050311), [right ventrolateral neuropil of A8](http://virtualflybrain.org/reports/VFB_00050309), [right centromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050445), [calyx of mushroom body](http://virtualflybrain.org/reports/VFB_00050502), [left ventromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050483), [left ventromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050484), [left centromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050476), [left centromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050482), [left centromedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050472), [right centromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050466), [right ventromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050450), [antennal lobe](http://virtualflybrain.org/reports/VFB_00050465), [superior lateral protocerebrum](http://virtualflybrain.org/reports/VFB_00050464), [right ventromedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050463), [right ventromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050461), [right ventromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050457), [left ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050487), [left ventromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050493), [left ventromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050495), [right ventromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050459), [right ventromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050460), [right ventromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050451), [right ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050455), [lateral appendix of mushroom body](http://virtualflybrain.org/reports/VFB_00050507), [left centrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050279), [left ventrolateral neuropil of T3](http://virtualflybrain.org/reports/VFB_00050489), [left ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050488), [right centrolateral neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050260), [left ventromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050490), [left centromedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050479), [left centrolateral neuropil of A1](http://virtualflybrain.org/reports/VFB_00050285), [right dorsomedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050414), [right centromedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050440), [left central neuropil of A6](http://virtualflybrain.org/reports/VFB_00050410), [left central neuropil of A7](http://virtualflybrain.org/reports/VFB_00050411), [right dorsomedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050413), [left centromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050477), [right centromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050444), [right centromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050447), [left centromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050468), [left centromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050475), [right ventromedial subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050449), [left centromedial neuropil of A4](http://virtualflybrain.org/reports/VFB_00050478), [left centromedial neuropil of mandibular segment](http://virtualflybrain.org/reports/VFB_00050469), [left centromedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050474), [clamp](http://virtualflybrain.org/reports/VFB_00050433), [right ventromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050452), [right centromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050436), [right ventrolateral neuropil of T2](http://virtualflybrain.org/reports/VFB_00050454), [right centromedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050446), [right ventrolateral neuropil of T1](http://virtualflybrain.org/reports/VFB_00050453), [right ventromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050456), [left centromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050467), [right dorsomedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050421), [right dorsomedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050422), [right centromedial neuropil of A1](http://virtualflybrain.org/reports/VFB_00050441), [left ventromedial neuropil of A2](http://virtualflybrain.org/reports/VFB_00050491), [left ventromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050496), [right dorsomedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050258), [right ventromedial neuropil of A3](http://virtualflybrain.org/reports/VFB_00050458), [right centrolateral subdivision of ventral nerve cord](http://virtualflybrain.org/reports/VFB_00050259), [left centrolateral neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050280), [superior medial protocerebrum](http://virtualflybrain.org/reports/VFB_00050276), [left centromedial neuropil of labial segment](http://virtualflybrain.org/reports/VFB_00050471), [right ventromedial neuropil of A7](http://virtualflybrain.org/reports/VFB_00050462), [left centromedial neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050470), [left central neuropil of A2](http://virtualflybrain.org/reports/VFB_00050406), [left central neuropil of maxillary segment](http://virtualflybrain.org/reports/VFB_00050400), [right dorsomedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050417), [left centromedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050473), [right ventromedial neuropil of tritocerebrum](http://virtualflybrain.org/reports/VFB_00050431), [right central neuropil of T2](http://virtualflybrain.org/reports/VFB_00050386), [right central neuropil of A1](http://virtualflybrain.org/reports/VFB_00050388), [right central neuropil of A5](http://virtualflybrain.org/reports/VFB_00050392), [anterior optic tubercle primordial](http://virtualflybrain.org/reports/VFB_00050430), [right centromedial neuropil of T1](http://virtualflybrain.org/reports/VFB_00050438), [right dorsomedial neuropil of A5](http://virtualflybrain.org/reports/VFB_00050424), [right dorsomedial neuropil of A6](http://virtualflybrain.org/reports/VFB_00050425), [right dorsomedial neuropil of A8](http://virtualflybrain.org/reports/VFB_00050427), [right dorsomedial neuropil of T3](http://virtualflybrain.org/reports/VFB_00050419), [right dorsomedial neuropil of T2](http://virtualflybrain.org/reports/VFB_00050418) | +| [JRC_FlyEM_Hemibrain](http://virtualflybrain.org/reports/VFB_00101384) | [PB(R3)](http://virtualflybrain.org/reports/VFB_00101491), [GOR(L)](http://virtualflybrain.org/reports/VFB_00101528), [BU(L)](http://virtualflybrain.org/reports/VFB_00101524), [LAL(L)](http://virtualflybrain.org/reports/VFB_00101526), [ATL(L)](http://virtualflybrain.org/reports/VFB_00101487), [GF(R)](http://virtualflybrain.org/reports/VFB_00101488), [PB(R1)](http://virtualflybrain.org/reports/VFB_00101489), [PB(R2)](http://virtualflybrain.org/reports/VFB_00101490), [VES(L)](http://virtualflybrain.org/reports/VFB_00101535), [NO1(R)](http://virtualflybrain.org/reports/VFB_00101543), [mALT(L)](http://virtualflybrain.org/reports/VFB_00101538), [CA(L)](http://virtualflybrain.org/reports/VFB_00101533), [PB(L6)](http://virtualflybrain.org/reports/VFB_00101503), [NO3(L)](http://virtualflybrain.org/reports/VFB_00101554), [PB(L8)](http://virtualflybrain.org/reports/VFB_00101505), [PB(L7)](http://virtualflybrain.org/reports/VFB_00101504), [SMP(L)](http://virtualflybrain.org/reports/VFB_00101507), [PB(L9)](http://virtualflybrain.org/reports/VFB_00101506), [gL(L)](http://virtualflybrain.org/reports/VFB_00101509), [SIP(L)](http://virtualflybrain.org/reports/VFB_00101508), [b\'L(L)](http://virtualflybrain.org/reports/VFB_00101511), [bL(L)](http://virtualflybrain.org/reports/VFB_00101510), [PB(R5)](http://virtualflybrain.org/reports/VFB_00101493), [CRE(L)](http://virtualflybrain.org/reports/VFB_00101512), [PB(R4)](http://virtualflybrain.org/reports/VFB_00101492), [PB(R7)](http://virtualflybrain.org/reports/VFB_00101495), [PB(R6)](http://virtualflybrain.org/reports/VFB_00101494), [PB(R8)](http://virtualflybrain.org/reports/VFB_00101496), [PB(L1)](http://virtualflybrain.org/reports/VFB_00101498), [PB(R9)](http://virtualflybrain.org/reports/VFB_00101497), [PB(L3)](http://virtualflybrain.org/reports/VFB_00101500), [PB(L2)](http://virtualflybrain.org/reports/VFB_00101499), [PB(L5)](http://virtualflybrain.org/reports/VFB_00101502), [PB(L4)](http://virtualflybrain.org/reports/VFB_00101501), [SCL(L)](http://virtualflybrain.org/reports/VFB_00101529), [SPS(L)](http://virtualflybrain.org/reports/VFB_00101532), [ICL(L)](http://virtualflybrain.org/reports/VFB_00101530), [RUB(L)](http://virtualflybrain.org/reports/VFB_00101515), [a\'L(L)](http://virtualflybrain.org/reports/VFB_00101514), [aL(L)](http://virtualflybrain.org/reports/VFB_00101513), [NO2(R)](http://virtualflybrain.org/reports/VFB_00101546), [NO3(R)](http://virtualflybrain.org/reports/VFB_00101548), [NO1(L)](http://virtualflybrain.org/reports/VFB_00101550), [NO2(L)](http://virtualflybrain.org/reports/VFB_00101553), [AL(L)](http://virtualflybrain.org/reports/VFB_00101484), [AOT(R)](http://virtualflybrain.org/reports/VFB_00101483), [GA(R)](http://virtualflybrain.org/reports/VFB_00101486), [POC](http://virtualflybrain.org/reports/VFB_00101485), [IPS(R)](http://virtualflybrain.org/reports/VFB_00101455), [SAD](http://virtualflybrain.org/reports/VFB_00101456), [GC](http://virtualflybrain.org/reports/VFB_00101478), [mALT(R)](http://virtualflybrain.org/reports/VFB_00101477), [AL(R)](http://virtualflybrain.org/reports/VFB_00101449), [VES(R)](http://virtualflybrain.org/reports/VFB_00101450), [SPS(R)](http://virtualflybrain.org/reports/VFB_00101454), [ATL(R)](http://virtualflybrain.org/reports/VFB_00101445), [IB](http://virtualflybrain.org/reports/VFB_00101443), [ICL(R)](http://virtualflybrain.org/reports/VFB_00101442), [GOR(R)](http://virtualflybrain.org/reports/VFB_00101453), [EPA(R)](http://virtualflybrain.org/reports/VFB_00101451), [CAN(R)](http://virtualflybrain.org/reports/VFB_00101459), [PRW](http://virtualflybrain.org/reports/VFB_00101460), [FLA(R)](http://virtualflybrain.org/reports/VFB_00101458), [GNG](http://virtualflybrain.org/reports/VFB_00101468), [CA(R)](http://virtualflybrain.org/reports/VFB_00101389), [LOP(R)](http://virtualflybrain.org/reports/VFB_00101388), [PED(R)](http://virtualflybrain.org/reports/VFB_00101390), [AMMC](http://virtualflybrain.org/reports/VFB_00101457), [b\'L(R)](http://virtualflybrain.org/reports/VFB_00101396), [LO(R)](http://virtualflybrain.org/reports/VFB_00101387), [ME(R)](http://virtualflybrain.org/reports/VFB_00101385), [AME(R)](http://virtualflybrain.org/reports/VFB_00101386), [a\'L(R)](http://virtualflybrain.org/reports/VFB_00101393), [aL(R)](http://virtualflybrain.org/reports/VFB_00101391), [bL(R)](http://virtualflybrain.org/reports/VFB_00101395), [RUB(R)](http://virtualflybrain.org/reports/VFB_00101440), [SCL(R)](http://virtualflybrain.org/reports/VFB_00101441), [SMP(R)](http://virtualflybrain.org/reports/VFB_00101437), [CRE(R)](http://virtualflybrain.org/reports/VFB_00101438), [ROB(R)](http://virtualflybrain.org/reports/VFB_00101439), [WED(R)](http://virtualflybrain.org/reports/VFB_00101419), [SLP(R)](http://virtualflybrain.org/reports/VFB_00101435), [LH(R)](http://virtualflybrain.org/reports/VFB_00101434), [SIP(R)](http://virtualflybrain.org/reports/VFB_00101436), [PVLP(R)](http://virtualflybrain.org/reports/VFB_00101416), [AVLP(R)](http://virtualflybrain.org/reports/VFB_00101408), [PLP(R)](http://virtualflybrain.org/reports/VFB_00101417), [AOTU(R)](http://virtualflybrain.org/reports/VFB_00101407), [PB](http://virtualflybrain.org/reports/VFB_00101401), [LAL(R)](http://virtualflybrain.org/reports/VFB_00101403), [FB](http://virtualflybrain.org/reports/VFB_00101398), [BU(R)](http://virtualflybrain.org/reports/VFB_00101402), [EB](http://virtualflybrain.org/reports/VFB_00101400), [gL(R)](http://virtualflybrain.org/reports/VFB_00101397), [AB(R)](http://virtualflybrain.org/reports/VFB_00101399), [AB(L)](http://virtualflybrain.org/reports/VFB_00102288), [EPA(L)](http://virtualflybrain.org/reports/VFB_00102287) | +| [JRC2018Unisex](http://virtualflybrain.org/reports/VFB_00101567) | [ICL](http://virtualflybrain.org/reports/VFB_00102179), [ROB](http://virtualflybrain.org/reports/VFB_00102174), [GOR](http://virtualflybrain.org/reports/VFB_00102214), [SLP](http://virtualflybrain.org/reports/VFB_00102162), [RUB](http://virtualflybrain.org/reports/VFB_00102175), [CRE](http://virtualflybrain.org/reports/VFB_00102171), [SMP](http://virtualflybrain.org/reports/VFB_00102170), [SPS](http://virtualflybrain.org/reports/VFB_00102215), [CAN](http://virtualflybrain.org/reports/VFB_00102275), [SCL](http://virtualflybrain.org/reports/VFB_00102176), [SIP](http://virtualflybrain.org/reports/VFB_00102164), [IB](http://virtualflybrain.org/reports/VFB_00102185), [ATL](http://virtualflybrain.org/reports/VFB_00102190), [AL](http://virtualflybrain.org/reports/VFB_00102201), [EPA](http://virtualflybrain.org/reports/VFB_00102213), [VES](http://virtualflybrain.org/reports/VFB_00102212), [LH](http://virtualflybrain.org/reports/VFB_00102159), [LO](http://virtualflybrain.org/reports/VFB_00102109), [SAD](http://virtualflybrain.org/reports/VFB_00102271), [AME](http://virtualflybrain.org/reports/VFB_00102108), [PVLP](http://virtualflybrain.org/reports/VFB_00102148), [AVLP](http://virtualflybrain.org/reports/VFB_00102146), [WED](http://virtualflybrain.org/reports/VFB_00102154), [PRW](http://virtualflybrain.org/reports/VFB_00102276), [AMMC](http://virtualflybrain.org/reports/VFB_00102273), [aL](http://virtualflybrain.org/reports/VFB_00102119), [LOP](http://virtualflybrain.org/reports/VFB_00102110), [a\'L](http://virtualflybrain.org/reports/VFB_00102121), [bL](http://virtualflybrain.org/reports/VFB_00102123), [ME](http://virtualflybrain.org/reports/VFB_00102107), [PED](http://virtualflybrain.org/reports/VFB_00102118), [CA](http://virtualflybrain.org/reports/VFB_00102114), [NO](http://virtualflybrain.org/reports/VFB_00102282), [GA](http://virtualflybrain.org/reports/VFB_00102281), [AOTU](http://virtualflybrain.org/reports/VFB_00102141), [BU](http://virtualflybrain.org/reports/VFB_00102139), [PLP](http://virtualflybrain.org/reports/VFB_00102152), [GNG](http://virtualflybrain.org/reports/VFB_00102280), [EB](http://virtualflybrain.org/reports/VFB_00102135), [LAL](http://virtualflybrain.org/reports/VFB_00102140), [PB](http://virtualflybrain.org/reports/VFB_00102137), [IPS](http://virtualflybrain.org/reports/VFB_00102218), [b\'L](http://virtualflybrain.org/reports/VFB_00102124), [gL](http://virtualflybrain.org/reports/VFB_00102133), [FB](http://virtualflybrain.org/reports/VFB_00102134), [FLA](http://virtualflybrain.org/reports/VFB_00102274) | + diff --git a/content/en/docs/Examples/_index.md b/content/en/docs/Examples/_index.md deleted file mode 100755 index 2ce72fd3..00000000 --- a/content/en/docs/Examples/_index.md +++ /dev/null @@ -1,11 +0,0 @@ - ---- -title: "Examples" -linkTitle: "Examples" -weight: 3 -date: 2017-01-05 -description: > - Examples of use cases for VFB or different data types that are available. ---- - - diff --git a/content/en/docs/Getting started/_index.md b/content/en/docs/Getting started/_index.md deleted file mode 100644 index f99cc936..00000000 --- a/content/en/docs/Getting started/_index.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -categories: ["Examples", "Placeholders"] -tags: ["test","docs"] -title: "Getting Started" -linkTitle: "Getting Started" -weight: 2 -aliases: ["/site/vfb_site/overview.htm"] -description: > - How to use the Virtual Fly Brain 3D browser ---- - -Below are a few overview pages to help you get started using VFB: diff --git a/content/en/docs/Getting started/overview.md b/content/en/docs/Getting started/overview.md deleted file mode 100644 index bb38df60..00000000 --- a/content/en/docs/Getting started/overview.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -categories: ["overview","help"] -tags: ["search","query","Anatomy","painted","domain","Template","Synaptic_neuropil"] -title: "Starting to explore VFB" -linkTitle: "Starting to explore" -description: > - Text search and query tools and how to explore the 3D images. -weight: 20 ---- - -VFB integrates data curated from the literature with image data from many bulk sources. The search system allows you to search for neurons and neuroanatomical structures using almost any name found in the literature. The query system can identify neurons innervating any specified neuropil or fasciculating with any specified tract. It also allows queries for genes, transgenes and phenotypes expressed in any brain region or neuron. Search and query results combine referenced textual descriptions with 3D images and links to originating data sources. VFB features tens of thousands of 3D images of neurons, clones and expression patterns, registered to standard template brains. Any combination of these images can be viewed together. A BLAST-type query system (NBLAST) allows you to find similar neurons and drivers starting from a registered neuron. - - Search for the item you're interested in - - Hover to explore brain regions in the Stack Viewer - - Query for related terms and images - -

- Virtual Fly Brain (VFB) Overview -

diff --git a/content/en/docs/Getting started/terminfo.md b/content/en/docs/Getting started/terminfo.md deleted file mode 100644 index 7acc3b77..00000000 --- a/content/en/docs/Getting started/terminfo.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -categories: ["overview","help"] -tags: ["term","tools"] -title: "This is the Term Info tab" -linkTitle: "Term Info" -description: > - Term Info displays information on the currently selected painted anatomy region, neuron, expression pattern or non-image term definitions -weight: 50 ---- - - - - Click on thumbnails to add that image to the viewer - - Click on terms to select them - - Click on download items to begin downloading - - Run term related queries - - -

- Virtual Fly Brain (VFB) 3D Viewer -

diff --git a/content/en/docs/Getting started/thumbnails.md b/content/en/docs/Getting started/thumbnails.md deleted file mode 100644 index 9d0939ba..00000000 --- a/content/en/docs/Getting started/thumbnails.md +++ /dev/null @@ -1,35 +0,0 @@ ---- -title: "How to Interpret VFB Thumbnails" -linkTitle: "Thumbnails" -tags: ["thumbnails","CD-MIP","MIP"] -weight: 100 -description: >- - VFB (Virtual Fly Brain) thumbnails are color depth maximum projection images that allow users to visualize the distribution of intensity values across different depths in a 3D image stack. ---- - -## How to Interpret VFB Thumbnails - -Here is a guide on how to interpret VFB thumbnails: - -- Each pixel in a VFB thumbnail corresponds to a specific depth in the image stack. -- Brighter or more intense colors indicate higher intensity values at that depth. -- The color bar on the right side of the image provides additional context about the mapping between color and depth. -- Each color in the color bar corresponds to a specific depth in the image stack, and the intensity of the color represents the maximum intensity value at that depth. -- Users can use the color bar to identify the depth of the signal and gain insights into the distribution of intensity values across different depths in the image stack. - - - -![Example VFB template thumbnail](https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnail.png) -* Note the colour bar and hence the signal in the image uses nealy the whole of the available (Z) stack space. - -![Example VFB neuron thumbnail](http://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png) -* Note the colour bar and hence the signal in the image uses less of the available (Z) stack space. - -![Example VFB flat neuron thumbnail](http://virtualflybrain.org/data/VFB/i/0000/0123/VFB_00101567/thumbnail.png) -* Note the colour bar and hence the signal in the image uses much less of the available (Z) stack space. - -In summary, VFB thumbnails provide a simplified way to visualize complex 3D image data. Each pixel's color and intensity represent the maximum intensity value at a specific depth, and the color bar provides additional context about the mapping between color and depth. By interpreting the colors and using the color bar, users can gain insights into the distribution of intensity values across the image stack. diff --git a/content/en/docs/Overview/_index.md b/content/en/docs/Overview/_index.md index f3812773..c0495a2f 100644 --- a/content/en/docs/Overview/_index.md +++ b/content/en/docs/Overview/_index.md @@ -3,7 +3,7 @@ title: "Overview" linkTitle: "Overview" weight: 1 description: > - An overview video showing some examples of what you can do with Virtual Fly Brain + An overview video showing some examples of what you can do with Virtual Fly Brain. --- {{< youtube id="z2Cre6avnpk" autoplay="true" >}} diff --git a/content/en/docs/Resources/_index.md b/content/en/docs/Resources/_index.md new file mode 100644 index 00000000..c93275c6 --- /dev/null +++ b/content/en/docs/Resources/_index.md @@ -0,0 +1,57 @@ +--- +title: "External Resources" +linkTitle: "Resources" +weight: 45 +description: > + External resources that may be useful to users of Virtual Fly Brain. + +--- + +## General Resources + +### [FlyBase](https://flybase.org) +Core database for Drosophila genetic information, including genes, tools, stocks, phenotypes, and literature references. + +FlyBase is in the process of transitioning into the [Alliance of Genome Resources (AGR)](https://www.alliancegenome.org/). + +### [NeuronBridge](https://neuronbridge.janelia.org/) +NeuronBridge is a tool search for neurons in Janelia FlyLight (LM) and FlyEM (EM) datasets. + +--- + +## EM Data Resources + +### [Codex](https://codex.flywire.ai/) +Connectome explorer developed at Princeton University. Hosts the BANC, MANC, optic-lobe, FAFB and male-cns datasets. Provides advanced search functions, a range of visualisations, and bulk data downloads. + +### [NeuPrint](https://neuprint.janelia.org) +Connectome explorer provided by Janelia Research Campus. Hosts the hemibrain, MANC, optic-lobe and male-cns datasets. Advanced search features are availble, including direct cypher queries of the neo4j database. Data is also accessible progammatically via [neuprint-python](https://github.com/connectome-neuprint/neuprint-python) or [neuprintr](https://natverse.org/neuprintr/). + +### [CATMAID](https://catmaid.org) +The Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is a web companion to the TrakEM2 software (Cardona, 2006) for management, registration and analysis of large-scale ssTEM datasets. + +{{< youtube id="CZpaTCuSQao" autoplay="true" title="A video introduction to catmaid software for connectomics from lead developer Tom Kazimiers hosted by the NEUBIAS Academy" >}} + +[CATMAID documentation](https://catmaid.readthedocs.io/en/stable/) + +[@catmaid on X](https://x.com/catmaid) + +--- + +## Light Microscopy Resources + +### [FlyLight](https://www.janelia.org/project-team/flylight) +The FlyLight Project at Janelia Research Campus produces large anatomical data sets and highly characterized collections of GAL4, LexA and Split-GAL4 drivers in order to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system. + +### [FlyLight Protocols](https://www.janelia.org/project-team/flylight/protocols) +Protocols used in the FlyLight project for dissection, staining and imaging of Drosophila central nervous systems. Also includes videos. + +### [larvalbrain](http://www.larvalbrain.org/#/) +Site for finding larval CNS driver lines via multiple query modes, including anatomy and intensity. + +--- + +## Single Cell Sequencing Resources + +### [EBI Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home) +The Single Cell Expression Atlas at the European Bioinformatics Institute (EBI) provides access to single cell RNA-seq data from multiple species, including Drosophila. diff --git a/content/en/docs/Tutorials/APIs/SOLR.md b/content/en/docs/Tutorials/APIs/SOLR.md index 4f3f844a..49f9b097 100644 --- a/content/en/docs/Tutorials/APIs/SOLR.md +++ b/content/en/docs/Tutorials/APIs/SOLR.md @@ -1,5 +1,5 @@ --- -title: "SOLR search example" +title: "Programmatic search using SOLR" linkTitle: "SOLR API" weight: 100 description: >- diff --git a/content/en/docs/Tutorials/APIs/0_VFB_API_overview.md b/content/en/docs/Tutorials/APIs/VFB_API_overview.md similarity index 97% rename from content/en/docs/Tutorials/APIs/0_VFB_API_overview.md rename to content/en/docs/Tutorials/APIs/VFB_API_overview.md index 8ee49351..51cda80e 100644 --- a/content/en/docs/Tutorials/APIs/0_VFB_API_overview.md +++ b/content/en/docs/Tutorials/APIs/VFB_API_overview.md @@ -1,6 +1,6 @@ --- title: "VFB connect API overview" -weight: 100 +weight: 1 series: ["API"] alias: ["/docs/tutorials/0_vfb_api_overview/"] date: 2021-12-27 @@ -15,7 +15,7 @@ The VFB connect API provides programmatic access to the databases underlying [Vi At the core of Virtual Fly Brain is a set of curated terms for Drosophila neuro-anatomy organised into a queryable classification, including terms for brain regions, e.g. [nodulus](http://virtualflybrain.org/reports/FBbt_00003680) and neurons e.g. [MBON01](http://virtualflybrain.org/reports/FBbt_00100234). These terms are used to annotate and classify individual brain regions and neurons in images and connectomics data. For example the term MBON01 is used to classify individual [neurons from sources including the CATMAID-FAFB and Neuprint-HemiBrain databases](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100234,ListAllAvailableImages). VFB stores both [registered 3D images](http://virtualflybrain.org/reports/VFB_00101382) and [connectomics data](https://v2-dev.virtualflybrain.org/org.geppetto.frontend/geppetto?q=VFB_00101382,ref_neuron_neuron_connectivity_query) (where available) for all of these neurons. -A single VfbConnect object wraps connections and canned queries against all open VFB databases. It includes methods for retreiving metadata about anatomy, individual brain regions and neurons including IDs for these that can be used for queries against other databases (e.g. CATMAID & neuprint). It provides methods for downloading images and connectomics data. It provides access to sophisticated queries for anatomical classes and individual neurons accoring to their classification & properties. +A single VfbConnect object wraps database connections and canned queries against all open VFB databases. It includes methods for retreiving metadata about anatomy, individual brain regions and neurons including IDs for these that can be used for queries against other databases (e.g. CATMAID & neuprint). It provides methods for downloading images and connectomics data. It provides access to sophisticated queries for anatomical classes and individual neurons according to their classification & properties. ### Locations for methods under a `VfbConnect` object. @@ -31,7 +31,7 @@ Note: available methods and their documentation are easy to explore in DeepNote. ### 1. `vc.neo_query_wrapper` methods overview -**1.1** `vc.neo_query_wrapper` TermInfo queries return the results of a VFB Term Information window as JSON, following the [VFB_JSON standard](), or a summary that can easily be converted into a DataFrame. +**1.1** `vc.neo_query_wrapper` TermInfo queries return the results of a VFB Term Information window as JSON, following the VFB_JSON standard, or a summary that can easily be converted into a DataFrame. ```python @@ -571,7 +571,7 @@ vc.neo_query_wrapper.xref_2_vfb_id(map(str, bodyIDs), db = 'neuprint_JRC_Hemibra ### 2. `vc` direct methods overview -**2.1** Methods that take the names of classes in VFB e.g. 'nodulus' or 'Kenyon cell', or simple query expressions using the names of classes and return metadata about the classes or individual neurons +**2.1** Methods that take the names of classes in VFB e.g. 'nodulus' or 'Kenyon cell', or simple query expressions using the names of classes and return metadata about the classes or individual neurons. ```python @@ -955,6 +955,4 @@ pd.DataFrame.from_records(KC_types) **2.2** Methods for querying connectivity -Please see [Connectivity Notebook](https://www.virtualflybrain.org/docs/tutorials/apis/connectome/4_connectomics/) for examples - - +Please see [Connectivity Notebook](/docs/past-workshops/connectome/4_connectomics) for examples. diff --git a/content/en/docs/Tutorials/APIs/_index.md b/content/en/docs/Tutorials/APIs/_index.md index c1d3d2a2..3a7acf84 100755 --- a/content/en/docs/Tutorials/APIs/_index.md +++ b/content/en/docs/Tutorials/APIs/_index.md @@ -1,10 +1,10 @@ --- -title: "Application Programming Interfaces (APIs)" -linkTitle: "APIs" -weight: 8 +title: "Application Programming Interface (API) Tutorials" +linkTitle: "API Tutorials" +weight: 20 date: 2021-12-27 series: ["API"] description: > - This is where we show you how to use VFBs Application Programming Interfaces (APIs) and other tools to explore the available data. + How to guides for the VFB Application Programming Interfaces (APIs). --- diff --git a/content/en/docs/Tutorials/APIs/1_datatypes.md b/content/en/docs/Tutorials/APIs/navis.md similarity index 93% rename from content/en/docs/Tutorials/APIs/1_datatypes.md rename to content/en/docs/Tutorials/APIs/navis.md index 554f5a63..44a65637 100644 --- a/content/en/docs/Tutorials/APIs/1_datatypes.md +++ b/content/en/docs/Tutorials/APIs/navis.md @@ -1,20 +1,16 @@ --- -title: "Data types" +title: "Exploring Neurons in Navis" weight: 110 series: ["API"] alias: ["/docs/tutorials/1_datatypes/"] date: 2021-12-27 description: > - In this notebook we will focus on neuron skeletons - a.k.a. `TreeNeurons` + How to explore the properties of `TreeNeurons` using navis. --- -# Overview -`navis` is a Python package for analysing, manipulating and visualizing neurons. - -`pymaid` lets you interface with a CATMAID server such as those hosted by VFB. - -Both packages have extensive documentation ([navis](https://navis.readthedocs.io/en/latest/) | [pymaid](https://pymaid.readthedocs.io/en/latest/)) with introductory tutorials, examples and a list of all available functions. +## Overview +`navis` is a Python package for analysing, manipulating and visualizing neurons. Official documentation [here](https://navis.readthedocs.io/en/latest/). ## Basic datatypes: neurons and neuron lists `navis` knows three types of neurons: @@ -129,9 +125,7 @@ n.id -There are many more properties that you might find interesting! In theory, you can use type `n.` and TAB to get auto-complete suggestions of available properties and methods. - -Deepnote appears to have problems with that sometimes - you can fall back to good 'ole `dir()` in that case. +There are many more properties that you might find interesting! Typing `n.` and pressing TAB should give auto-complete suggestions of available properties and methods. If your notebook editor has problems with that, you can fall back to using `dir()`. Here is an (incomplete) list of some of the more relevant properties: - `bbox`: bounding box of the neuron @@ -139,13 +133,12 @@ Here is an (incomplete) list of some of the more relevant properties: - `id`: every neuron has an ID - `nodes`: the SWC node table underlying the neuron -And a couple of class methods: +And some class methods: - `reroot`: reroot neuron -- `plot2d`/`plot3d`: plot the neuron (see also subsequent lessons) +- `plot2d`/`plot3d`: plot the neuron (see also [plotting turorial](/docs/tutorials/apis/plotting/)) - `copy`: make and return a copy - `prune_twigs`: remove small terminal twigs -At this point I encourage you to just explore and play around with what TreeNeuron has to offer. Also check out the [docs](https://navis.readthedocs.io/en/latest/source/tutorials/generated/navis.TreeNeuron.html#navis.TreeNeuron)! As an example: this is how you get the ID of this neuron's root node. @@ -162,7 +155,7 @@ n.root -Some of the properties such as `.root` or `.ends` are computed on-the-fly from the underlying raw data. For `TreeNeurons` that's the node table (and it's graph representation). The node table is a pandas DataFrame that looks effectively like a SWC: +Some of the properties such as `.root` or `.ends` are computed on-the-fly from the underlying raw data. For `TreeNeurons` that's the node table (and its graph representation). The node table is a pandas DataFrame that looks effectively like a SWC: ```python diff --git a/content/en/docs/Tutorials/APIs/4_nblast.md b/content/en/docs/Tutorials/APIs/nblast.md similarity index 99% rename from content/en/docs/Tutorials/APIs/4_nblast.md rename to content/en/docs/Tutorials/APIs/nblast.md index e4c2fafd..80cf69a5 100644 --- a/content/en/docs/Tutorials/APIs/4_nblast.md +++ b/content/en/docs/Tutorials/APIs/nblast.md @@ -9,15 +9,18 @@ description: > NBLAST is a method to quantify morphological similarity. --- -# NBLAST +## Overview + NBLAST (Costa et al., 2016) is a method to quantify morphological similarity. It works on "dotprops" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison (i.e. a perfect match would be 1). ![nblast](https://github.com/schlegelp/navis/raw/master/docs/_static/NBLAST_neuron_comparison.png) +## Finding Matching Neurons + VFB computes NBLAST scores for all neurons in its database. So if all you want is a list of similar neurons, it's fastest (and easiest) to get those directly from VFB. -``` +``` python # Import libs and initialise API objects from vfb_connect.cross_server_tools import VfbConnect import navis.interfaces.neuprint as neu @@ -31,10 +34,10 @@ vc = VfbConnect() client = neu.Client('https://neuprint.janelia.org', dataset='hemibrain:v1.1') ``` -First let's write a little function to grab VFB neurons and turn them into `navis` neurons. This is modified from `vc.neo_query_wrapper.get_images`. +First let's write a function to grab VFB neurons and turn them into `navis` neurons. This is modified from `vc.neo_query_wrapper.get_images`. -``` +``` python import requests from tqdm import tqdm @@ -77,7 +80,7 @@ def get_vfb_neurons(vfb_ids, template='JRC2018Unisex'): ``` -``` +``` python # Search for similar neurons using the VFB ID of an ellipsoid body neuron in FAFB # We got that ID from a search on the VFB website similar_to_EPG6L1 = vc.get_similar_neurons('VFB_001012ay') @@ -157,7 +160,7 @@ similar_to_EPG6L1 -``` +``` python # Read those neurons from VFB query = get_vfb_neurons('VFB_001012ay') matches = get_vfb_neurons(similar_to_EPG6L1.id.values) @@ -166,7 +169,7 @@ matches = get_vfb_neurons(similar_to_EPG6L1.id.values) -``` +``` python matches ``` @@ -268,7 +271,7 @@ matches -``` +``` python # Define colors such that query is black import seaborn as sns colors = ['k'] + sns.color_palette('muted', len(matches)) @@ -294,14 +297,16 @@ navis.plot3d([query, matches], color=colors) -So that looks decent! +These like a good match! -Next: Let's say you have a set of neurons and you want to group them into morphologically similar "types". To demonstrate this, we will take ellipsoid body (protocerebral bridge) neurons from VFB and cluster them using NBLAST. +## Clustering Groups of Neurons +Now imagine you have a set of neurons and you want to group them into morphologically similar "types". To demonstrate this, we will take some ellipsoid body neurons from VFB and cluster them using NBLAST. -``` -# Find instances of EB-PB neurons -eb_pb_ids = pd.DataFrame.from_records(vc.get_instances("eb-pb-vbo neuron")) + +``` python +# Find instances of EB-PB-gall neurons +eb_pb_ids = pd.DataFrame.from_records(vc.get_instances("adult ellipsoid body-protocerebral bridge-gall neuron")) eb_pb_ids.head() ``` @@ -417,7 +422,7 @@ eb_pb_ids.head() -``` +``` python # Get the neurons from VFB eb_pb = get_vfb_neurons(eb_pb_ids.id.values) eb_pb @@ -531,24 +536,20 @@ eb_pb -Now that we have the skeletons, we need to turn them into dotprops. Couple things to keep in mind: +Now that we have the skeletons, we need to turn them into dotprops. Keep in mind that: 1. NBLAST is optimized for data in microns. Since our neurons are in the `JRC2018Unisex` template, they already are. 2. Neurons should have the same sampling rate (i.e. nodes per micron). To ensure this we will resample the neurons to 1 point per micron. 3. We won't be doing this this time around but we typically simplify the neurons slightly by e.g. pruning small twigs (`navis.prune_twigs()`) to reduce noise. -``` +``` python eb_dps = navis.make_dotprops(eb_pb, resample=1, k=5) -# Note this neuronlist contains dotprops now +# Note this NeuronList /contains dotprops now eb_dps ``` - - - -