How to use ROICaT

TRACKING:

• Online App: Good for first time users. Try it out without installing anything.

• Interactive notebook (also available in colab) $~$

• Command line interface script:

roicat --pipeline tracking --path_params /path/to/params.yaml --dir_data /folder/with/data/ --dir_save /folder/save/ --prefix_name_save expName --verbose

CLASSIFICATION:

• Interactive notebook - Drawing. (also available in colab) $~$: $~~$ Use mouse to draw circles around regions of a UMAP to classify ROIs.

• Interactive notebook - Simple interactive Labeling: $~~$ Images of ROIs are displayed and you use the keyboard to manually label them.

• Interactive notebook - Interactive labeling with drawing: $~~$ Draw circles around regions of a UMAP to subselect ROIs for manual labeling.

• Interactive notebook - Train classifier

• Interactive notebook - Inference with classifier

OTHER:

• Custom data importing notebook

• Use the API to integrate ROICaT functions into your own code: Documentation.

• Run the full tracking pipeline using the CLI or roicat.pipelines.pipeline_tracking with default parameters generated from roicat.util.get_default_parameters() saved as a yaml file.