A lesson teaching the fundamentals of analysing image data acquired via light microscopy experiments.
This lesson focuses on the use of napari, 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.
Contributions are very welcome - please make a suggestion or correct an error by raising an issue.
See the CONTRIBUTING.md file for contribution guidelines.
These lessons were initially developed as part of the Health and Biosciences IDEAS project, which is a training initiative funded by UKRI Innovation Scholars (MR/V03863X/1).
Continued support for this project is provided in part by the UKRI Digital Research Skills Catalyst. The Catalyst Project is funded by UKRI Digital Research Infrastructure Programme from October 2024 to March 2027. Project reference: UKRI/ST/B000299/1.
This course is developed using the Carpentries Workbench. The sandpaper R package is the main driver used to configure and build the website (see installation instructions below).
For a comprehensive guide on how to use sandpaper, check out the documentation.
When making changes, please create a new branch and open a Pull Request. Don't
push directly to main.
## Create new branch
git checkout main
git pull origin main
git switch -c <username>/<my_awesome_edits>The basic workflow looks something like this (it's recommended, though not necessary, to run this in RStudio):
## Add new episode in plain Markdown format (use `create_episode_Rmd` for RMarkdown)
sandpaper::create_episode_md("Episode name")
## ...... Edit new episode md contents ......
## Preview site
sandpaper::serve()
## ...... Make further changes, the website preview should update automatically ......
## ...... Rinse and repeat ......When you're happy, commit, push and open a PR on GitHub. This will trigger the
sandpaper PR validation and preview
workflows to
validate and preview the new content. Once the PR gets approved, merge it into
main and wait for the github actions to complete, after which the updates
should be visible on the
website
The sandpaper package is used to build the lesson website. We created a fork of varnish to style the lesson website with IDEAS branding.
To install these forks locally, run the following from within an R session:
## Install devtools
install.packages("remotes")
## Install HealthBioscienceIDEAS/varnish
remotes::install_github("HealthBioscienceIDEAS/varnish", dependencies = TRUE)Then to build the lesson locally, from within the microscopy-novice directory, run
sandpaper::build_lesson()That should open the built home page in a browser window automatically, but
if not, you can find the built HTML files in the site/ directory.