HCR Analysis files

Installation

First, we recommend to create a new conda environment with

conda create -n HCR python=3.9

And activate it with conda activate HCR and install requirements with:

pip install -r requirements

Files Documentation

• main.py: This is the principal file that extracts the main statistics from the HCR images. It has two sub commands:

  • process: Process our standardized directory structure writing an output .csv file and saving auxiliary images at the input images directory.

  • figure: Create images of intermediate steps from the process function.

• apply_threshold.py: Applies a threshold from the metadata file to the TBXT and SOX2 measurements selecting the cells which express both and save it to the input images directory.

• rename.py: Renames and reorganizes the files to our standard format using the metadata file.

• store_metadata.py: Auxiliary file to map metadata from table to the standardized directory path.

• max_project_figures.py: Creates the images of the maximum intensity projections overlaid with the selected cells.

• count_plot.Rmd: Generates the count barplot given the processed measurements file and the threshold annotation file. File must be edited to set input paths.