This repository contains code linked to pre-publication work of .... The code contained within has been developed to generate metrics and report the image quality coming from he Cytiva/Leica INCEll MxIF Microscope.
Clone this Repository:
git clone https://github.com/smujiang/MxIF_DAPI_ref_QC.git
Configure your Python enviroment:
#Check Version (> 3.7.x):
python --version
#Install Dependancies:
pip install --upgrade -r requirements.txt
Filename: run_dapi_ref_qc.py
Purpose: This python script is intended to automatically evaluate MxIF image qualities using DAPI rounds as reference.
- QC reports will be created, including json and html versions.
- Intermedia evaluation metrics will be saved for advanced users.
CLI: python run_dapi_ref_qc.py -i <path to processor dir> -o <path to output dir> -c <case id to be evaluated>
We also compared the cell distribution differences between high-quality group (HQ, FOVs passed our QC) and low-quality group (LQ, FOVs failed our QC).
We found that in stroma cell,
- LQ group presented higher density in some region (elevated more than 20%).
- HQ and LQ group share similar cell distribution, that's because:
a) there are “high quality” sub-regions within LQ FOVs;
b) there are undetected LQ FOVs within HQ group