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@labsyspharm Laboratory of Systems Pharmacology @ Harvard

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    173 repositories

    • minerva-core-ui

      Public
      A microscopy viewer for non-experts
      JavaScript
      •
      MIT License
      •3•0•10•2•Updated Oct 23, 2025Oct 23, 2025

    • cycif.importer

      Public
      R
      •
      Other
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • gater

      Public
      JavaScript
      •
      MIT License
      •3•1•4•1•Updated Oct 23, 2025Oct 23, 2025

    • minerva_analysis

      Public
      JavaScript
      •
      MIT License
      •8•27•22•4•Updated Oct 23, 2025Oct 23, 2025

    • peripheral-neuropathy

      Public
      0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • okl-analysis

      Public
      Python
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • PCa

      Public
      Spatial analysis of the prostate TME
      R
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • mccellpose

      Public
      Alternative interface to the Cellpose cell segmentation algorithm that uses constant memory
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • 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 Oct 9, 2025Oct 9, 2025

    • cdk7-analysis

      Public
      R
      •0•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • harvardtissueatlas

      Public
      Harvard Tissue Atlas website
      SCSS
      •5•3•3•0•Updated Oct 2, 2025Oct 2, 2025

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •61•136•65•2•Updated Oct 2, 2025Oct 2, 2025

    • cellcutter

      Public
      Create thumbnails of cells in a given image.
      Python
      •
      MIT License
      •5•4•0•0•Updated Sep 29, 2025Sep 29, 2025

    • ad-personalized

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • basicpy-docker-mcmicro

      Public
      Python
      •4•0•0•0•Updated Sep 24, 2025Sep 24, 2025

    • 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 Sep 18, 2025Sep 18, 2025

    • vae

      Public
      Python
      •
      MIT License
      •2•3•0•0•Updated Sep 17, 2025Sep 17, 2025

    • ad-rna-editing

      Public
      R
      •1•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • aws-tools

      Public
      General purpose scripts for managing our AWS usage
      Shell
      •
      MIT License
      •0•1•0•0•Updated Sep 15, 2025Sep 15, 2025

    • minerva-cloud-ui

      Public
      Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •2•2•1•5•Updated Sep 10, 2025Sep 10, 2025

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •12•31•4•0•Updated Sep 2, 2025Sep 2, 2025

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •7•29•7•1•Updated Sep 2, 2025Sep 2, 2025

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •48•152•56•10•Updated Aug 11, 2025Aug 11, 2025

    • ome-tiff-pyramid-tools

      Public
      Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.
      Python
      •
      MIT License
      •8•17•0•1•Updated Aug 8, 2025Aug 8, 2025

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

      Public
      Custom codes for Vallius, Shi, Novikov et al. manuscript 2025
      Jupyter Notebook
      •1•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • 2025_Williams_Pant_Melanoma-TRM

      Public
      Python
      •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • vae-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•3•0•0•Updated Jul 7, 2025Jul 7, 2025

    • mel-3d-mis

      Public
      MATLAB
      •2•4•0•0•Updated Jul 4, 2025Jul 4, 2025

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonpypispatial-analysisimage-analysissingle-cell-analysis
      Python
      •
      MIT License
      •32•100•47•2•Updated Jun 30, 2025Jun 30, 2025

    • orion-crc

      Public
      MATLAB
      •
      MIT License
      •4•20•2•0•Updated Jun 24, 2025Jun 24, 2025