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README.md

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Raw

This folder contains the scripts and data to reproduce the result in the paper "A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology"

You can find the raw data here: https://doi.org/10.5281/zenodo.6784251.

Organization

Notebooks

"notebooks" folder contains jupyter notebook script used:

  • 01 Processing of IMC (protein) and SIMS (metabolite) images
  • 02 Registration of IMC and SIMS images for different imaging regions
  • 03 Single-cell level segmentation and visualization of segmentation masks
  • 04 Single-cell level intensity extraction and single-cell proteomics clustering
  • 05 VAE joint embedding of protein and metabolite modalities
  • 06 Metabolite analysis in different regions (metabolite difference, distance analysis, competition analysis)
  • 07 VAE comparison at patient level from lung cancer
  • 08 Trajectory analysis
  • 09 Protein metabolite correlation analysis
  • 10 Large FOV analysis of metabolite expression
  • 11 Segmentation of single-cell with Mesmer pipeline
  • 12 Comparison of registration from IMC and SIMS modalities

Source code

"src" folder contains customs scripts used:

  • affine transformation
  • "utils.py" contains plotting and io custom functions
  • "spatial" folder contains custom code for spatial interaction functions
  • "scSpaMet" folder contains keras code used for VAE analysis