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Multi-Well Tools

Tools to extract data produced by multi-well microscope experiments i.e. Nautilus

Run the script from the command line

> python /path/to/well_data.py /path/to/json_config --input_video_path /path/to/input/video --output_dir_path /path/to/output/dir

args with a leading -- are optional and if supplied will override keys with the same name in the json config.

Basic System Test

To run a basic system test, if you are in the main directory (multiwell_tools) :

> python ./src/well_data.py ./test_data/config.json/ --input_video_path ./test_data/MantarrayMiniPlate1Twitch.avi

This will run the well data extraction function which will produce:

  • xlsx files with the time series data from each well,
  • a zip archive of all the xlsx files,
  • an image with the roi's drawn on one frame of the input video,
  • a plot of every wells time series data.