Home

ColonySelector

A Gui for semi-automated colony counting and also fix the clustering by hand. It relies on PyQtGraph, a pure-Python graphics library, for fast manipulations of the data.

Requirements

All packages needed to run the Gui are in environment.yml. You can set up an environment for the Gui with the following command line: For Windows make sure you use the Anaconda Prompt.

conda env create -f path/to/environment.yml 

Now activate the environment:

conda activate ColonyEnv

For some reason PyQt5 needs to be pip installed: link

pip install PyQt5

Make sure you are using Python 3.8+ (the environment create will satisfy this):

python --version

Optional

Images can be converted from .tif to .jpg to reduce the size and improve speed. To do this run convert_jpg.py by changing the path to path/to/tif/folder/*.tif. Viewing the image while selecting colonies is preferred but optional, as is explained in "How to Run?".

How to Run?

The data needs to be saved as a two column (x,y) dataframe with .pkl format. Some clear examples can be found in the pandas API reference here. Use the test_data to get the Gui running and as a template. Open the Gui.py and go to the "User defined Paths:" and change the paths to the test_data. If you are on a Windows use "C:/path/to/test_data" format, this will avoid errors.

To run the Gui:

python path/to/ColonySelector_Gui.py

You should now see the Gui! For information on how to use the Gui go to How to use?.