image-analysis-field-guide
Scientific image analysis resources and examples.
https://github.com/epfl-center-for-imaging/image-analysis-field-guide
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Keywords
Repository
Scientific image analysis resources and examples.
Basic Info
- Host: GitHub
- Owner: EPFL-Center-for-Imaging
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://imaging.epfl.ch/field-guide/
- Size: 47.9 MB
Statistics
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
The Image Analysis Field Guide
Essential toolkit to get started in scientific image analysis.
👉 See the live website at this URL.
Help us improve the site
✒️ Do you have any comments about our site? Don't hesitate to share them via this Google Form.
🤝 Contributions to our project are very welcome. See our Contributing Guide for more details.
Installation
Option 1: Install and build the Jupyter book website locally
Install the packages required to build the jupyter book website:
pip install -r requirements.txt
Install the scientific packages required to run the notebooks:
pip install -r jupyterhub/sections/spawn-image/requirements.txt
Build the Jupyter book:
jupyter-book build src/
Then, drag and drop _build/html/index.html in a web browser.
To check external links:
jb build src --builder linkcheck
Option 2: Build and run with docker
Build the image:
docker build --build-arg NOTION_KEY=$NOTION_KEY -t $(whoami)/$(basename ${PWD}) .
Run the jupyter book in a container on http://localhost:8080/.
Quick test:
docker run --rm -it -p 8080:80 $(whoami)/$(basename ${PWD}):latest
Persistent:
docker run -dp 8080:80 --name image-analysis-field-guide $(whoami)/$(basename ${PWD}):latest
Set up a JupyterHub and link it to the site
We provide a configuration to set up and run a JupyterHub for users and contributors. The JupyterHub can be linked to the website via the jupyterhub_url parameter in _config.yml. Users can run notebooks in the Jupyter Hub environment via the launch icon.
Build and run the JupyterHub
From the jupyterhub/ directory:
docker compose up -d
This command will
- Build the ./jupyterhub/spawn-image/Dockerfile.
- Build the ./jupyterhub/Dockerfile.jupyterhub.
- Run the JupyterHub on
http://localhost:8000/.
Our JupyterHub configuration is derived from JupyterHub Imaging.
Owner
- Name: EPFL-Center-for-Imaging
- Login: EPFL-Center-for-Imaging
- Kind: organization
- Repositories: 1
- Profile: https://github.com/EPFL-Center-for-Imaging
Citation (CITATION.cff)
authors:
- family-names: Wittwer
given-names: Mallory
cff-version: 1.2.0
message: "If you use this software, please cite it using the metadata from this file."
title: "The Image Analysis Field Guide"
repository-code: "https://github.com/EPFL-Center-for-Imaging/image-analysis-field-guide"
date-released: "2024-01-12"
keywords:
- "image analysis"
license: BSD-3-Clause
GitHub Events
Total
- Watch event: 4
Last Year
- Watch event: 4
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mallory Wittwer | m****r@e****h | 52 |
| Mallory Wittwer | 3****r | 1 |
| Mallory Wittwer | w****r@d****4 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- ubuntu latest build
- itables *
- jupyter-book *
- jupyterlab *
- jupyterlab_myst *
- jupytext *
- matplotlib *
- napari *
- napari-skimage-regionprops *
- python-dotenv *
- seaborn *
- skan *
- spam *
- stardist-napari *
- trackpy *
- hub/jupyterhub-field-guide-spawn-image latest
- jupyterhub latest
- quay.io/jupyter/pytorch-notebook x86_64-ubuntu-22.04 build
- dask-labextension *
- itables *
- jupyter-ai *
- jupyter-archive *
- jupyter-book *
- jupyter-resource-usage *
- jupyter-server-proxy *
- jupyter-videochat *
- jupyter_app_launcher *
- jupyterlab-git ==0.50.0
- jupyterlab-logout *
- jupyterlab-lsp *
- jupyterlab-rise *
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- jupytext *
- langchain-openai *
- lckr_jupyterlab_variableinspector *
- nbgitpuller *
- nbsphinx *
- python-lsp-server *
- sidecar *
- sphinx-gallery *
- PyWavelets *
- cookiecutter *
- dask-image *
- graphviz *
- imagecodecs *
- matplotlib *
- napari *
- napari-skimage-regionprops *
- opencv-python *
- plotly *
- seaborn *
- seaborn-image *
- skan *
- spam *
- stackview *
- stardist-napari *
- trackpy *