Overview

This page is intended to provide a quick overview of the workflow. For more information please see the User Guide

Typical Set of function calls to preprocess data

Most important functions have (will soon have) help. To view the help run the function simply as:

First format data by calling

convert_to_hdf5.py path/to/datafolder/

Next motion register data

motion_register_data.py path/to/hdf5.h5

Then draw ROIs either manually

ROI_Drawer.py path/to/hdf5.h5

or automatically

run_roi_finder.py finder_name path/to/hdf5.h5

followed by manul curation using the "ROI_Drawer"

Then, if the data contains several separate acquisition runs involving the same cells

share_roiinfo.py path/to/hdf5.h5

Finally extract traces from the cells:

extract_roi_traces.py path/to/hdf5.h5

General Advice

The key functions defining the pipeline are run by calling (via command line)

python /path/to/twoptb/twoptb/scripts/generic_script.py -h