Introduction

cuisto is an open-source Python package aiming at facilitating the quantification of histological data, eg. the characterization of objects of interest in 2D images such as cells or neuronal processes revealed by immunohistochemistry or endogenously fluorescent proteins in brain slices.

It leverages QuPath measurements export to collate data from different slices and subjects, derive quantifying metrics within regions of interest, compute spatial distributions and generate graphs, featuring human-readable configuration files to easily customize cuisto behavior to best match your use-case.

In theory, cuisto should work with any measurements table with the required columns, but has been designed with QuPath in mind, especially used alongisde ABBA to align 2D images on a reference brain atlas.

For atlas-related features, including ontology-based blacklisting and structures contours drawing for heatmaps, cuisto relies on the Brainglobe Atlas API, thus supporting all atlases packaged in Brainglobe.

After ABBA registration of 2D histological slices and QuPath objects' detection, cuisto is used to :

• compute metrics, such as objects density in each brain regions,
• compute objects distributions in three three axes (rostro-caudal, dorso-ventral and medio-lateral),
• compute averages and sem across animals,
• display all the above.

cuisto processing abilities revolve around two QuPath core concepts, Annotations (regions of interest) and Detections (objects of interest). The repository hosting the cuisto package provides QuPath utility scripts to help you process and format the data within QuPath before export.

This documentation covers the whole process depicted above, including cuisto installation instructions, ABBA installation instructions, guides to prepare images for the pipeline, detect objects with QuPath, register 2D slices on a 3D atlas with ABBA, and cuisto usage along with examples.

Due to the IT environment of the laboratory, this documentation is very Windows-oriented but most of it should be applicable to Linux and MacOS as well by slightly adapting terminal commands.

Documentation navigation

The documentation outline is on the left panel, you can click on items to browse it. In each page, you'll get the table of contents on the right panel.

Useful external resources

• Project repository : https://github.com/TeamNCMC/cuisto
• QuPath documentation : https://qupath.readthedocs.io/en/stable/
• Aligning Big Brain and Atlases (ABBA) documentation : https://abba-documentation.readthedocs.io/en/latest/
• Brainglobe : https://brainglobe.info/
• BraiAn, a similar project featuring a dedicated QuPath extension : https://silvalab.codeberg.page/BraiAn/
• Image.sc community forum : https://forum.image.sc/
• Introduction to Bioimage Analysis, an interactive book written by QuPath's creator : https://bioimagebook.github.io/index.html

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.

The documentation itself is built with MkDocs using the Material theme.