cuisto

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.

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 :

   conda create -n cuisto-env python=3.12
   

4. Activate the environment :

   conda activate cuisto-env
   

5. Install cuisto :

   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 :

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 :

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.