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    38 repositories

    • 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.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • macsima2mc

      Public
      utitilies for macsima image sets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•3•0•Updated Nov 11, 2024Nov 11, 2024

    • macsima_pipeline

      Public
      Shell
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • micronuclAI

      Public
      Automated identification of micronuclei for chromosomal instability (CIN) quantification.
      Python
      •
      GNU Affero General Public License v3.0
      •1•7•0•0•Updated Oct 15, 2024Oct 15, 2024

    • mi_spatialomics

      Public
      Data analysis for “Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration”
      Jupyter Notebook
      •
      MIT License
      •1•2•3•1•Updated Oct 9, 2024Oct 9, 2024

    • Segmentation_prep

      Public
      Image preprocessing for different segmentation approaches.
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 17, 2024Sep 17, 2024

    • nf-core-test-datasets

      Public
      Test data to be used for automated testing with nf-core pipelines hosted on SchapiroLabor
      MIT License
      •353•0•0•0•Updated Sep 7, 2024Sep 7, 2024

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •58•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • projectionpursuit

      Public
      projection pursuit clustering
      Python
      •
      MIT License
      •2•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • phenoimager2mc

      Public
      Formatting tif/ome-tif metadata for MCMICRO staging modules
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • mask2bbox

      Public
      Useful tools for converting segmentation masks into bounding box objects.
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Aug 9, 2024Aug 9, 2024

    • imc2mc

      Public
      staging of imc images for mcmicro
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • stardist

      Public
      StarDist - Object Detection with Star-convex Shapes
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •220•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •4•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • quantification

      Public
      Quantification module for mcmicro
      Python
      •13•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • micronuclAI_streamlit

      Public
      This repository contains a streamlit app for CIN inferences based on the micronuclAI tool
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•1•0•Updated Jul 9, 2024Jul 9, 2024

    • spot2cell

      Public
      Tool to assign FISH spots to their corresponding cell
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Jun 25, 2024Jun 25, 2024

    • norm_methods

      Public
      A single repo of all available/potential tabular normalization methods for downstream analysis of spatial proteomics datasets.
      Jupyter Notebook
      •1•2•0•0•Updated Jun 12, 2024Jun 12, 2024

    • micronuclAI_labeling

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 29, 2024May 29, 2024

    • mcmicro-celesta

      Public
      CELESTA phenotyping module for MCMICRO
      R
      •0•2•0•0•Updated Mar 20, 2024Mar 20, 2024

    • scimap

      Public
      This is a repo that will implement scimap from labsyspharm/scimap and add CLI for different tools
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 20, 2024Mar 20, 2024

    • molkart-local

      Public
      Repository for local modules used in nf-core/molkart
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • Background_subtraction

      Public
      Background subtraction for COMET platform
      Python
      •
      MIT License
      •3•6•5•0•Updated Nov 21, 2023Nov 21, 2023

    • mcmicro_QC

      Public
      Module to prepare QC output from MCMICRO for MultiQC.
      HTML
      •
      MIT License
      •2•1•0•0•Updated Sep 25, 2023Sep 25, 2023

    • histoCAT

      Public
      Histology Topography Cytometry Analysis Toolbox
      MATLAB
      •
      Other
      •23•66•39•0•Updated Aug 21, 2023Aug 21, 2023

    • mcmicro_nfcore_demo

      Public
      A small demo workflow for MCMICRO using only nf-core modules. Result of the March 2023 nf-core hackathon.
      HTML
      •
      MIT License
      •0•1•0•0•Updated May 31, 2023May 31, 2023

    • MindaGap

      Public
      Fill empty grids of a panorama made from several tiles with sensefull values (mean of imediate neighbourhood)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Jan 17, 2023Jan 17, 2023

    • mcmicro_hackathon_2022

      Public
      Website for the MCMICRO hackathon 2022
      nextflowimage-processingmcmicro
      HTML
      •
      MIT License
      •14•0•0•0•Updated Oct 24, 2022Oct 24, 2022

    • tools-mti

      Public
      Python
      •
      MIT License
      •7•0•0•0•Updated Oct 5, 2022Oct 5, 2022

    • KBestak_Lab-rotation

      Public
      Lab rotation report 2/2022 – 4/2022, Krešimir Beštak
      image-stitchingimage-registrationcycifsegmentation
      ImageJ Macro
      •0•1•0•0•Updated May 4, 2022May 4, 2022