Skip to content

Expand readme and remove UCL-specific links #116

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
K-Meech merged 4 commits into from
May 5, 2026
Merged

Expand readme and remove UCL-specific links #116

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
05e9085
expand the readme with info about the lesson and funding acknowledgem…
K-Meech May 1, 2026
56aa6cf
fix links and remove UCL-specific references
K-Meech May 1, 2026
46c5a8f
update life cycle stage to beta
K-Meech May 1, 2026
24b3dd1
move globias description to new line
K-Meech May 1, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 22 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,24 @@
# microscopy-novice
# Image Analysis with Napari 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

Expand Down Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
11 changes: 7 additions & 4 deletions episodes/additional-resources.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,18 @@ 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/)
Expand Down
4 changes: 1 addition & 3 deletions index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Loading