Using cuisto

Prerequisites checklist

Prior to use cuisto, check that you have :

• installed cuisto
• set up a QuPath project
• detected objects of interest as Detections in the QuPath project
• made sure Detections are properly formatted : their classification is in the form object type: marker
• added atlas coordinates to Detections as measurements called "Atlas_X", "Atlas_Y" and "Atlas_Z" in millimeters (mm) (to plot spatial distributions only)
• Annotations (regions of interest), either with ABBA or custom ones
• made sure Annotations are properly formatted, including a classification formatted as Hemisphere: Name
• added measurements to the Annotations. The measurements are properly formatted : their name is in the form object type: marker measurement name
• exported the Annotations and Detections measurements as tables, either as individual files (one file per subject) or following the directory structure if using the pipeline mode

Usage

Configuration

Retrieve a copy of the config_template.toml file located in the configs folder, as well as atlas-related configuration files in the atlas folder. Edit them according to your need.

More details about those files are given in the configuration section.

Examples

If the quantification process was done following the full pipeline guideline (including following the directory structure), check this code snippet or check the demo notebook showcasing a minimal example here.

Alternatively, if you have only one data table exported from QuPath (thus one animal), check the cells quantification or the fibers coverage examples.

In the event you have several QuPath project that should be pooled together to average metrics across animals but did not follow the expected directory structure, export the annotations measurements tables (and the detections if spatial distributions are of interest) from QuPath. Then, check the Batch-process animals section and the example script batch_process_animal.py located in the examples folder.