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@SchapiroLabor

Schapiro Lab

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  1. histoCAT histoCAT Public

    Histology Topography Cytometry Analysis Toolbox

    MATLAB 67 23

  2. micronuclAI micronuclAI Public

    Automated identification of micronuclei for chromosomal instability (CIN) quantification.

    Jupyter Notebook 9 2

  3. Background_subtraction Background_subtraction Public

    Background subtraction for COMET platform

    Python 6 4

  4. macsima2mc macsima2mc Public

    utitilies for macsima image sets

    Python 4 3

  5. mi_spatialomics mi_spatialomics Public

    Data analysis for “Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration”

    Jupyter Notebook 3 1

  6. Segmentation_prep Segmentation_prep Public

    Image preprocessing for different segmentation approaches.

    Python 3

Repositories

Showing 10 of 51 repositories
  • macsima2mc Public

    utitilies for macsima image sets

    SchapiroLabor/macsima2mc’s past year of commit activity
    Python 4 BSD-3-Clause 3 5 0 Updated Apr 2, 2025
  • codex2mc Public Forked from mbruhns/codex2mc

    utitilies for codex image sets

    SchapiroLabor/codex2mc’s past year of commit activity
    Python 0 BSD-3-Clause 3 0 0 Updated Apr 2, 2025
  • NEP_scimap Public

    Pairwise neighbor preference analysis using scimap for comparison between methods

    SchapiroLabor/NEP_scimap’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 31, 2025
  • NEP_IMCRtools Public

    histoCAT used from IMCR tools for SCNA

    SchapiroLabor/NEP_IMCRtools’s past year of commit activity
    R 0 MIT 0 0 0 Updated Mar 31, 2025
  • nfcore_mcmicro Public Forked from nf-core/mcmicro

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    SchapiroLabor/nfcore_mcmicro’s past year of commit activity
    Nextflow 0 MIT 18 0 0 Updated Mar 25, 2025
  • mi_spatialomics_minerva_story_d1 Public

    This repository contains the Minerva story for a 1 day post-MI sample attached to the Spatial multi-omics of myocardial infarction manuscript.

    SchapiroLabor/mi_spatialomics_minerva_story_d1’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Mar 21, 2025
  • NEP_MistyR Public

    Misty run on cell types for SCNA

    SchapiroLabor/NEP_MistyR’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 21, 2025
  • NEP_comparison Public

    Systematic comparison of spatial cellular neighborhood analysis (SCNA) tools in the course of my master thesis.

    SchapiroLabor/NEP_comparison’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Mar 21, 2025
  • NEP_IST_generation Public

    In silico tissue generation for generation of tissue cohorts for SCNA comparison

    SchapiroLabor/NEP_IST_generation’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Mar 20, 2025
  • NEP_Squidpy Public

    Test squidpy neighborhood enrichment function

    SchapiroLabor/NEP_Squidpy’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 19, 2025
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