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@labsyspharm Laboratory of Systems Pharmacology @ Harvard

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    187 repositories

    • minerva-core-ui

      Public
      A microscopy viewer for non-experts
      TypeScript
      •
      MIT License
      •4•1•13•5•Updated Sep 25, 2026Sep 25, 2026

    • mccellpose

      Public
      Alternative interface to the Cellpose cell segmentation algorithm that uses constant memory
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•2•0•Updated Sep 24, 2026Sep 24, 2026

    • okl-analysis

      Public
      Python
      •1•0•0•0•Updated Sep 23, 2026Sep 23, 2026

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
      •
      MIT License
      •16•16•29•1•Updated Sep 23, 2026Sep 23, 2026

    • visinity

      Public
      JavaScript
      •
      MIT License
      •5•17•8•0•Updated Sep 22, 2026Sep 22, 2026

    • minerva-public-website

      Public
      Public Website for information on Minerva software suite
      Creative Commons Zero v1.0 Universal
      •0•0•1•0•Updated Sep 21, 2026Sep 21, 2026

    • Chen-Santagata-Kidney-2026

      Public
      MATLAB
      •
      MIT License
      •2•0•0•0•Updated Sep 18, 2026Sep 18, 2026

    • ome-tiff-pyramid-tools

      Public
      Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.
      Python
      •
      MIT License
      •8•18•0•1•Updated Sep 17, 2026Sep 17, 2026

    • ad-rna-editing

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Sep 14, 2026Sep 14, 2026

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •64•156•64•3•Updated Sep 14, 2026Sep 14, 2026

    • Volumetric-CyCIF

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 13, 2026Sep 13, 2026

    • 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.
      microscopyomeminerva
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •6•4•2•4•Updated Sep 9, 2026Sep 9, 2026

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonpypispatial-analysis
      pythonpypispatial-analysisimage-analysissingle-cell-analysis
      Python
      •
      MIT License
      •38•116•47•6•Updated Sep 9, 2026Sep 9, 2026

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •12•65•7•1•Updated Sep 7, 2026Sep 7, 2026

    • vae

      Public
      Python
      •
      MIT License
      •2•4•0•0•Updated Aug 28, 2026Aug 28, 2026

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •15•36•1•0•Updated Aug 28, 2026Aug 28, 2026

    • cellcutter

      Public
      Create thumbnails of cells in a given image.
      Python
      •
      MIT License
      •5•4•0•0•Updated Aug 28, 2026Aug 28, 2026

    • minerva_analysis

      Public
      JavaScript
      •
      MIT License
      •8•27•22•4•Updated Aug 27, 2026Aug 27, 2026

    • mcmicro-lsp

      Public
      mcmicro helpers for local use within the LSP (especially O2)
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 15, 2026Aug 15, 2026

    • stic-ms-2026

      Public
      Gray Precancer Atlas v 2.0_KADER_Santagata Lab
      R
      •0•0•0•0•Updated Aug 14, 2026Aug 14, 2026

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •57•181•61•13•Updated Aug 7, 2026Aug 7, 2026

    • Zhao-FMSAE-2026

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Aug 4, 2026Aug 4, 2026

    • Image-Analysis-Guides

      Public
      mostly single cell image analysis and instructions for relevant tasks related to our imaging platform
      Jupyter Notebook
      •0•0•0•0•Updated Jul 31, 2026Jul 31, 2026

    • 2025-Vallius-Shi-Novikov-melanoma-PCAII

      Public
      Custom codes for Vallius, Shi, Novikov et al. manuscript 2025
      Jupyter Notebook
      •1•0•0•0•Updated Jun 30, 2026Jun 30, 2026

    • GBM-Lactylation-Santagata-Lab

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 30, 2026Jun 30, 2026

    • cdk7-analysis

      Public
      R
      •0•0•0•0•Updated Jun 24, 2026Jun 24, 2026

    • TB-3D-TLS-2026

      Public
      Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis
      Jupyter Notebook
      •0•1•0•0•Updated Jun 24, 2026Jun 24, 2026

    • Amiryousefi-Wala-Prostate-2026

      Public
      Spatial analysis of the prostate TME
      R
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • ad-personalized

      Public
      TYK2 mediates neuroinflammation in dementia with Alzheimer’s disease
      R
      •
      MIT License
      •0•0•0•0•Updated May 29, 2026May 29, 2026

    • Santagata-Ependymoma-2026

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 21, 2026May 21, 2026
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