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https://github.com/bodenmillergroup/misegmentation

Analyzing the performance of the ImcSegmentationPipeline

https://github.com/bodenmillergroup/misegmentation

Science Score: 26.0%

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    Found 5 DOI reference(s) in README
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Repository

Analyzing the performance of the ImcSegmentationPipeline

Basic Info
  • Host: GitHub
  • Owner: BodenmillerGroup
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 1.5 MB
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  • Watchers: 5
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Created over 5 years ago · Last pushed over 5 years ago
Metadata Files
Readme License

README.md

WIP analysis workflow: MISegmentation

Snakemake Build Status

This is a workflow that should compare segmentation performance of single cell segmentation masks generated via the ImcSegmentationPipeline (https://github.com/BodenmillerGroup/ImcSegmentationPipeline).

Authors

  • Vito RT Zanotelli (@votti)

Datasets

This repository will host the segmentation performance comparison for 5 published dataset that were processed with the ImcSegmentationPipeline.

  • 'Schulz2017': "Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry", DOI: 10.1016/j.cels.2017.12.001

    • Data in Data/SegData/Her2_TMA

      • Ilp: 20161212Her2TMA_2.ilp
      • Cpproj: 20170116Her2TMA2expandandpropagate_comparison.cpproj
      • Panel: panel.csv
      • analysis_stacks: analysis
      • ometiffs: ometiff
      • random crops: available

      => extracted labels look good and usable

      -> Good to go!

  • 'Damond2018': "A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry", DOI: 10.1016/j.cmet.2018.11.014

    • Data in: CM2017

      • ILP: CM2017cellsNEW.ilp
      • Cpproj: CellsAndStructures_v1.1.cpproj
      • Panel: CM_Panel.csv
      • ometiff: ometiff
      • analysis_stacks: analysis -> only full stacks
      • random crops: via file names

      -> Good to go!

  • 'Ali2020': "The single-cell pathology landscape of breast cancer", DOI: 10.1038/s41586-019-1876-x

    • Raw data: from aspera ~/.aspera/connect/bin/ascp -TQ -l40m -P 33001 -i "./asperawebiddsa.openssh" idr0076@fasp.ebi.ac.uk:. .
    • Contains masks, full stack and pannel
    • Also have .ilp - but naming entierly different.

    • Data in: metabrik

      • ILP: metabricnewclassifier_20180108.ilp
      • Cpproj: 2segmentilastikv2gradedannularmasks.cpproj
      • Panel: metabricpanelforanalysisstacks.csv
      • ometiff: ??
      • analysisstacks: analysisstacks -> full stacks only
      • random crops: via file names => naming is standardized but ome files still missing

      -> No go

  • 'Jackson2020': "The single-cell pathology landscape of breast cancer", DOI: 10.1038/s41586-019-1876-x

    • Data in: basel_zuri

      • Ilp: 20171130pixelclassificationBaselZuri.ilp
      • cpproj: 20180102BaselZuri_segmentation.cpproj
      • Panel: ??
      • ometiffs: ome
      • analysisstacks: analysisstacks
      • random crops: ilastik_random, no crop coordinates in filenames -> Had to get some data from the archive -> naming with exception of 4 -> fixed by matching

      -> Good to go!

  • 'HubMAP2020': "The Human Body at Cellular Resolution: the NIH Human BioMolecular Atlas Program" DOI: 10.1038/s41586-019-1629-x

    • Data: HuBMAP/Data/20191211analysisHubMAPLNSpleen_thymus

      • cpproj: ??
      • Panel: 20191128_HubMAP.csv
      • ometiffs: ometiffiles
      • analyis_stacks: tiffs
      • random crops: ilastik

      -> Good to go! d

Owner

  • Name: BodenmillerGroup
  • Login: BodenmillerGroup
  • Kind: organization

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