Calcium Signal Propagation speed analysis pipeline

Used in the paper "Multi-chamber cardioids unravel human heart development and cardiac defects" to analyse the speed of calcium signal propagation in cardioids. Most of the algorithms are present in the calsipro package, with some in calsiprovis.library. The rest of calsiprovis is the interactive web application, based on rapids and runnel. runnel starts a webserver and provides all necesarry tools to start python in a browser, whereas rapids has some helper functions to have applications run with runnel. Finally hoernchen is an sqlite-based ORM.

For analysis use the calsipro functions or use the calsiprovis CLI. To run the interactive web application build all the python packages with poetry, create a python environment with all packages installed and run:

runnel PATH_TO_RAPIDS_WHEEL PATH_TO_CALSIPROVIS_WHEEL--foreground=calsiprovis.app:run --pyodide-dir=./src/runnel/pyodide/ --foreground-arg=PATH_TO_EXPERIMENT_REFS --background=rapids.socket.backend:run

where PATH_TO_EXPERIMENT_REFS points to file containing all experiments in a json format [{'name': 'plate1', 'path': 'PATH_TO_EXPERIMENT_FILE'}, ...]. The individual experiment files can be created and manipulated with commands provided by the calsiprovis CLI. Three commands add CZI files to the experiment: add_gcamp, add_fluro and add_brightfield, for details see the individual commands.