1. System requirements

• Code should be able to run in any computer capable of running the Anaconda Python Distribution
• Code was tested using the python packages described in requirements.txt in a Windows10 system

2. Installation instructions

• Make sure you have a python3 installation (Anaconda distribution recommended)
• Install python package requirements included in the requirements.txt file (using a new python environment is recommended)

3. Demo and usage Instructions:

• Use measure2kymographs.py to measure the angle of 2 kymographs:

  • script will ask the user to select one kymograph at a time
  • then it will print in the terminal the angles of both kymographs and ask the user where it should save resulting images

• Use batchanalysis.py to measure the kymographs of several cells:

  • script will ask for a folder containing cells to measure
  • folder structure should be the same as in the example folder (included in the zip file)
    • each Cell folder should be name Cell_X, with X being cell number
    • for each cell, the batch script expects the folder to contain the kymographs (kym1 and kym2) and a crop of the cell containing the lines used to generate the kymographs (kymline1 and kymline2)
  • then inside the selected folder it will save an html report containing the result of the analysis

• Both options can be used to test the code using the example data in the "example" folder

  • expected result can be seen in the file "report.html" contained in the example folder

• Code execution should take less than 1 minute for batches of less than 1000 cells

Copyright (c) 2020, Bacterial Cell Biology Lab, ITQB-NOVA All rights reserved.

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