readme.md

Introduction

This repository is a Python program to organize the output of microscope.

It is recommended to open the project in Pycharm in the Microscope computer, go to main.py, and then click the green run button near if __name__ == "__main__":.

Main

This file contains code for organizing files based on position numbers. Multi-channel microwell array images are sorted over a time course into folders for each position.

Config

This file contains parameters for file organization. root_directory is an address to provide input. LOOP is the number of positions in a microwell array, always 240. ROUND is the number of loops of imaging. This code calls main to run the file organization.

Test with Mock Data

Since the real microscope images are very large, it would be convient to make a reduplication of the data but only with the file names. In Windows, it can be done by

robocopy \mydir \mydir_structure /create /e