A python-based pipeline for analyzing whole-slide imaging mass cytometry (WS-IMC) data from pancreatic ductal adenocarcinoma (PDAC).
Completed on behalf of Campbell Lab at the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital.
This repository contains an end-to-end pipeline for analyzing whole-slide imaging mass cytomegry (IMC-WS) images in pancreatic ductal adenocarcinoma (PDAC) datasets.
- single-cell segmentation is not possible, pixel-level data
- trained CNN on (insert stats) WS-IMC and (insert stats) TMA-IMC images for feature extraction of sliding windows
- evaluate information gain/adequacy of TMA-based approaches for assessing spatial heterogeneity
...
The pipeline consists of the following main steps:
1. Configuration:
2. Preprocessing:
3. Feature Extraction
4. Clustering:
5. Downstream Analysis:
6. Evaluation of TMA-IMC: