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    156 repositories

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •58•113•56•2•Updated Dec 4, 2024Dec 4, 2024

    • cycif.org

      Public
      cycif.org GitHub Pages Website
      JavaScript
      •
      MIT License
      •9•2•4•4•Updated Nov 27, 2024Nov 27, 2024

    • minerva-browser

      Public
      JavaScript
      •
      MIT License
      •5•4•10•3•Updated Nov 27, 2024Nov 27, 2024

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonspatial-analysisimage-analysissingle-cell-analysispypi
      Python
      •
      MIT License
      •26•77•36•2•Updated Nov 26, 2024Nov 26, 2024

    • harvardtissueatlas

      Public
      Harvard Tissue Atlas website
      SCSS
      •6•3•2•0•Updated Nov 26, 2024Nov 26, 2024

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •42•129•54•12•Updated Nov 25, 2024Nov 25, 2024

    • prostate

      Public
      Analysis of prostate cancer CyCIF data
      R
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • stic-ms-2024

      Public
      Custom codes related to Kader, Lin, Hug manuscript 2024
      R
      •1•0•0•1•Updated Nov 22, 2024Nov 22, 2024

    • minerva-core-ui

      Public
      A microscopy viewer for non-experts
      TypeScript
      •
      MIT License
      •2•0•10•2•Updated Nov 21, 2024Nov 21, 2024

    • minerva-author-ui

      Public
      Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •5•4•2•4•Updated Nov 21, 2024Nov 21, 2024

    • omero-oauth

      Public
      OMERO.web application to allow OAuth2 login to OMERO
      Python
      •
      GNU Affero General Public License v3.0
      •3•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • ad-rna-editing

      Public
      R
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • okl-analysis

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

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •4•20•4•2•Updated Nov 3, 2024Nov 3, 2024

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
      •
      MIT License
      •14•15•19•1•Updated Nov 1, 2024Nov 1, 2024

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •12•25•0•1•Updated Oct 31, 2024Oct 31, 2024

    • mcmicro-lsp

      Public
      mcmicro helpers for local use within the LSP (especially O2)
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • sarek-variant-calling-pipeline

      Public
      Shell
      •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • mcqc

      Public
      Quality control module for mcmicro
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • ad-personalized

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • vae-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Oct 4, 2024Oct 4, 2024

    • beta-segmentinator

      Public
      Python
      •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • gater

      Public
      JavaScript
      •
      MIT License
      •3•1•1•1•Updated Sep 16, 2024Sep 16, 2024

    • minerva_analysis

      Public
      JavaScript
      •
      MIT License
      •6•26•21•4•Updated Sep 16, 2024Sep 16, 2024

    • mel-3d-mis

      Public
      MATLAB
      •1•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • plateviewer

      Public
      Renders HTS microscopy image data into a Minerva Story for visual review
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Sep 3, 2024Sep 3, 2024

    • ludwigtumoratlas.org

      Public
      Ludwig Tumor Atlas website
      SCSS
      •1•1•0•1•Updated Aug 27, 2024Aug 27, 2024

    • quantification

      Public
      Quantification module for mcmicro
      Python
      •13•9•6•1•Updated Aug 9, 2024Aug 9, 2024

    • biospecimen-disease-research-terminology

      Public
      Clinical disease terminology for annotation of biospecimen records
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • minerva-ui-mockup

      Public
      Mockup design with Improved UI/UX for creating Minerva stories
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 18, 2024Jul 18, 2024