This repository is used for the acquisition, pre-processing, and analysis of IMC data during the DQBM Block-Course 2024. It is explicitly tailored to handle acquisition of the same ROIs from consecutive sections using the compressed and uncompressed antibody panels.
## Structure: The repository is structured into three major directories.
- Contains the bio-image analysis scripts to perform semi-automated region-selection for IMC acquisition using IF images.
- Contains Python-Scripts to pre-process IMC data and perform cell segmentation.
- Contains R-scripts to analyze data.
- Spillover Compensation, Data Transformation, Quality Control, Cell Annotation
- Comparison of compressed and Uncompressed dataset.
Check DirectoryStructure.md for how to organize your directory structure including data and code!