Data

Tools

Indexes

Applications

Experiments

Open Source Science

cuisto

cuisto: A Python package to quantify neurohistological data from QuPath and ABBA - Published in JOSS (2025)

https://github.com/teamncmc/cuisto

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation ·

Repository

Quantify histological data

Basic Info
Statistics
  • Stars: 5
  • Watchers: 0
  • Forks: 2
  • Open Issues: 2
  • Releases: 16
Created over 1 year ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

cuisto

Python Version PyPI Tests status

Python package for histological quantification of objects in reference atlas regions.

cuisto uses data exported from QuPath used with ABBA to pool data and derive, average and display metrics.

Graphs generated with cuisto

Check the full documentation : https://teamncmc.github.io/cuisto

Install

Steps 1-3 below need to be performed only once. If Anaconda or conda is already installed, skip steps 1-2 and use the Anaconda prompt instead. 1. Install Miniforge, as user, add conda to PATH and make it the default interpreter. 2. Open a terminal (PowerShell in Windows). run : conda init and restart the terminal. 3. Create a virtual environment named "cuisto-env" with Python 3.12 : bash conda create -n cuisto-env python=3.12 4. Activate the environment : bash conda activate cuisto-env 5. Install cuisto : bash pip install cuisto 6. (Optional) Download the latest release from here (choose "Source code (zip)) and unzip it on your computer. You can copy the scripts/ folder to get access to the QuPath and Python scripts. You can check the notebooks in docs/demo_notebooks as well !

The cuisto package will be then available in Python from anywhere as long as the cuisto-env conda environment is activated. You can get started by looking and using the Jupyter notebooks.

For more detailed installation instructions, see the documentation.

Update

To update, simply activate your environment (conda activate cuisto-env) and run : bash pip install cuisto --upgrade

Usage

See the Quick start section in the documentation.

Using notebooks

Some Jupyter notebooks are available in the docs/demo_notebooks folder. You can open them in an IDE (such as vscode with the Jupyter extension, select the "cuisto-env" environment as kernel in the top right) or in the Jupyter web interface (jupyter notebook in the terminal, with the "cuisto-env" environment activated).

Brain structures

You can generate brain structures outlines coordinates in three projections (coronal, sagittal, top-view) with the cuisto.atlas module (see usage example here). They are used to overlay brain regions outlines in 2D projection density maps. It requires a lot of RAM to generate them and might take a while. Those files have been pre-generated for some atlases, they are available in the separate brain-structures repository. They are automatically downloaded (if available) before plotting.

Build the doc

To build and look at the documentation offline : Download the repository, extract it and from the command line in the cuisto-main folder, run : bash pip install .[doc] Then, run : mkdocs serve Head to http://localhost:8000/ from a web browser. The documentation is built with MkDocs using the Material theme. KaTeX CSS and fonts are embedded instead of using a CDN, and are under a MIT license.

Contributing

See Contributing.

Credits

cuisto has been primarly developed by Guillaume Le Goc in Julien Bouvier's lab at NeuroPSI. The clever name was found by Aurélie Bodeau.

Owner

  • Name: TeamNCMC
  • Login: TeamNCMC
  • Kind: organization
  • Location: France

Julien Bouvier lab at the Paris-Saclay Institute of Neuroscience

JOSS Publication

cuisto: A Python package to quantify neurohistological data from QuPath and ABBA
Published
July 03, 2025
DOI
Volume 10, Issue 111, Page 7906
Authors
Guillaume Le Goc ORCID
Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France
Alexis d'Humières ORCID
Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France
Antoine Lesage ORCID
Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France
Julien Bouvier ORCID
Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France
Editor
Adam Tyson ORCID
Tags
histology immunochemistry microscopy image analysis neuroscience
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
authors:
- family-names: Le Goc
  given-names: Guillaume
  orcid: "https://orcid.org/0000-0002-6946-1142"
- family-names: d'Humières
  given-names: Alexis
  orcid: "https://orcid.org/0009-0006-3860-2084"
- family-names: Lesage
  given-names: Antoine
  orcid: "https://orcid.org/0009-0000-7362-3215"
- family-names: Bouvier
  given-names: Julien
  orcid: "https://orcid.org/0000-0002-1307-4426"
contact:
- family-names: Bouvier
  given-names: Julien
  orcid: "https://orcid.org/0000-0002-1307-4426"
doi: 10.5281/zenodo.15684283
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Le Goc
    given-names: Guillaume
    orcid: "https://orcid.org/0000-0002-6946-1142"
  - family-names: d'Humières
    given-names: Alexis
    orcid: "https://orcid.org/0009-0006-3860-2084"
  - family-names: Lesage
    given-names: Antoine
    orcid: "https://orcid.org/0009-0000-7362-3215"
  - family-names: Bouvier
    given-names: Julien
    orcid: "https://orcid.org/0000-0002-1307-4426"
  date-published: 2025-07-03
  doi: 10.21105/joss.07906
  issn: 2475-9066
  issue: 111
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7906
  title: "cuisto: A Python package to quantify neurohistological data
    from QuPath and ABBA"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07906"
  volume: 10
title: "cuisto: A Python package to quantify neurohistological data from
  QuPath and ABBA"

GitHub Events

Total
  • Create event: 21
  • Issues event: 16
  • Release event: 10
  • Watch event: 5
  • Delete event: 6
  • Issue comment event: 16
  • Push event: 148
  • Pull request review comment event: 10
  • Pull request review event: 17
  • Pull request event: 42
  • Fork event: 1
Last Year
  • Create event: 21
  • Issues event: 16
  • Release event: 10
  • Watch event: 5
  • Delete event: 6
  • Issue comment event: 16
  • Push event: 148
  • Pull request review comment event: 10
  • Pull request review event: 17
  • Pull request event: 42
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 10
  • Total pull requests: 24
  • Average time to close issues: 27 days
  • Average time to close pull requests: about 8 hours
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.6
  • Average comments per pull request: 0.0
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 24
  • Average time to close issues: 27 days
  • Average time to close pull requests: about 8 hours
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.6
  • Average comments per pull request: 0.0
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PolarBean (6)
  • IgorTatarnikov (4)
Pull Request Authors
  • GuillaumeLeGoc (15)
  • Crackodu91 (9)
  • adamltyson (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 44 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 12
  • Total maintainers: 1
pypi.org: cuisto

Quantification of objects in histological slices

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 44 Last month
Rankings
Dependent packages count: 9.9%
Average: 32.7%
Dependent repos count: 55.6%
Maintainers (1)
guielge
Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
pyproject.toml pypi
  • brainglobe-atlasapi >=2.0.7
  • brainglobe-heatmap >=0.5.4
  • brainrender >=2.1.14
  • geojson >=3.1.0
  • h5py >=3.11
  • ipykernel *
  • ipympl *
  • ipywidgets *
  • matplotlib >=3.9.0
  • notebook *
  • numpy >=2
  • orjson >=3.10.3
  • pandas [performance]>2.2.2
  • paquo >=0.8.0
  • scikit-image >0.22.0
  • seaborn >=0.13.2
  • shapely >=2.0.4
  • skan >=0.12.0
  • tifffile >=2024.4.24
  • tqdm *
  • typer *