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