Cellpose-Quantification

A repository for single-cell quantification using mask formats generated by cellpose!

Getting Started

Installing Dependancies

• Clone this git repository locally
• Setup Python environment and install packages

pip install -r requirements.txt

Executing program

This program can be run from the command line with the following example command:

python RunQuantification-CLI.py ./path/to/images ./path/to/masks markers.csv 

With Normalisation

python RunQuantification-CLI.py ./path/to/images ./path/to/masks markers.csv --norm log

Expected Parameters

• ./path/to/image
  • Can take Input from a directory containing tiff images
• ./path/to/masks
  • Can take a directory .npy, .png, and .tif masks as inputs generated by cellpose
• markers.csv
  • The path to metadata relating to markers corresponding to each markers, formatted on one row e.g. CD45, DAPI, Ki67, etc
• --norm
  • An optional parameter which defines a normalisation technique to use, current implementation allows: minmax and log normalisation.

Authors

Please cite this git page when using this tool! Miles Bailey
@milesbailey121