From 05e908572e37fd860dbda848d0969ea7e1625f63 Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Fri, 1 May 2026 16:06:22 +0100 Subject: [PATCH 1/4] expand the readme with info about the lesson and funding acknowledgements --- README.md | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 015d15c5..9df2ecfd 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,24 @@ -# microscopy-novice +# Image Analysis for Microscopy - This is the lesson repository for microscopy-novice +A lesson teaching the fundamentals of analysing image data acquired via light microscopy experiments. + +## Lesson Content + +This lesson focuses on the use of [napari](https://napari.org/), a Python-based image viewer, for all image processing steps. +It also covers the basics of how to design a light microscopy experiment and optimise acquisition settings for a given research question. + +## Contribution + +Contributions are very welcome - please make a suggestion or correct an error by [raising an issue](https://github.com/HealthBioscienceIDEAS/microscopy-novice/issues). + +See the [CONTRIBUTING.md file](CONTRIBUTING.md) for contribution guidelines. + +## Acknowledgements + +These lessons were initially developed as part of the [Health and Biosciences IDEAS](https://healthbioscienceideas.github.io/) project, which is a training initiative funded by [UKRI Innovation Scholars](https://www.ukri.org/opportunity/innovation-scholars-data-science-training-in-health-bioscience/) (MR/V03863X/1). + +Continued support for this project is provided in part by the [UKRI Digital Research Skills Catalyst](https://digitalskillscatalyst.ac.uk/). +The Catalyst Project is funded by UKRI Digital Research Infrastructure Programme from October 2024 to March 2027. Project reference: UKRI/ST/B000299/1. ## Development @@ -41,9 +59,8 @@ When you're happy, commit, push and open a PR on GitHub. This will trigger the [*sandpaper* PR validation and preview workflows](https://carpentries.github.io/sandpaper-docs/pull-request.html) to validate and preview the new content. Once the PR gets approved, merge it into -`main` and wait for the [Build and -Deploy](https://github.com/HealthBioscienceIDEAS/microscopy-novice/actions/workflows/sandpaper-main.yaml) -action to complete, after which the updates should be visible on the +`main` and wait for the github actions to complete, after which the updates +should be visible on the [website](https://healthbioscienceideas.github.io/microscopy-novice/) ### Building the lesson locally From 56aa6cf5ec85ff13633e5e48d46f56e4ba516fdc Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Fri, 1 May 2026 16:17:42 +0100 Subject: [PATCH 2/4] fix links and remove UCL-specific references --- README.md | 2 +- episodes/additional-resources.md | 10 ++++++---- index.md | 4 +--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 9df2ecfd..7b7c8e04 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Image Analysis for Microscopy +# Image Analysis with Napari for Microscopy A lesson teaching the fundamentals of analysing image data acquired via light microscopy experiments. diff --git a/episodes/additional-resources.md b/episodes/additional-resources.md index 9171890b..a678b7d5 100644 --- a/episodes/additional-resources.md +++ b/episodes/additional-resources.md @@ -73,15 +73,17 @@ principles. ### Talks/seminars about image processing -- [UCL Bioimage interest group](https://www.ucl.ac.uk/lmcb/ucl-biig) -Monthly talks (in person and online) about image analysis of biological images. -Open to all. - - [Eurobioimaging virtual pub ](https://www.eurobioimaging.eu/about-us/virtual-pub) Weekly online talks on various topics related to microscopy and image analysis. Open to all. +- [Global BioImage Analysts' Society (GloBIAS) seminar series](https://www.globias.org/activities/bia-seminar-series-2025-2026) Online talks on bio-image analysis. Open to all. + +- [UCL Bioimage interest group](https://www.ucl.ac.uk/science-technology-platforms/imaging/ucl-bioimage-interest-group) +Monthly talks (in person and online) about image analysis of biological images. +Open to all. + ### Python - [Software carpentry python course ](https://swcarpentry.github.io/python-novice-inflammation/) diff --git a/index.md b/index.md index 10d45cff..fbb64fb0 100644 --- a/index.md +++ b/index.md @@ -17,9 +17,7 @@ work with light microscopy imaging data in their research projects. - No python experience is necessary or assumed, but you will get more out of the course if you know some basics e.g. from the online [Software Carpentry -python course](https://swcarpentry.github.io/python-novice-inflammation/) or -[an in-person course at UCL -](https://www.ucl.ac.uk/advanced-research-computing/education/training). +python course](https://swcarpentry.github.io/python-novice-inflammation/). - Please bring a laptop (Windows, Mac or Linux) to the lesson. Before the start of the course, please follow the [setup instructions](learners/setup.md) so From 46c5a8f2dc9d5795ab3415952cd2c6a0cfae999e Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Fri, 1 May 2026 16:23:51 +0100 Subject: [PATCH 3/4] update life cycle stage to beta --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 104161e7..23db6581 100644 --- a/config.yaml +++ b/config.yaml @@ -21,7 +21,7 @@ keywords: 'software, data, lesson, The Carpentries' # Life cycle stage of the lesson # possible values: pre-alpha, alpha, beta, stable -life_cycle: 'pre-alpha' +life_cycle: 'beta' # License of the lesson materials (recommended CC-BY 4.0) license: 'CC-BY 4.0' From 24b3dd1da105bcda9fb0ba612f06ce638ca20606 Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Fri, 1 May 2026 16:36:34 +0100 Subject: [PATCH 4/4] move globias description to new line --- episodes/additional-resources.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/episodes/additional-resources.md b/episodes/additional-resources.md index a678b7d5..2359d2cf 100644 --- a/episodes/additional-resources.md +++ b/episodes/additional-resources.md @@ -78,7 +78,8 @@ principles. Weekly online talks on various topics related to microscopy and image analysis. Open to all. -- [Global BioImage Analysts' Society (GloBIAS) seminar series](https://www.globias.org/activities/bia-seminar-series-2025-2026) Online talks on bio-image analysis. Open to all. +- [Global BioImage Analysts' Society (GloBIAS) seminar series](https://www.globias.org/activities/bia-seminar-series-2025-2026) +Online talks on bio-image analysis. Open to all. - [UCL Bioimage interest group](https://www.ucl.ac.uk/science-technology-platforms/imaging/ucl-bioimage-interest-group) Monthly talks (in person and online) about image analysis of biological images.