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@labsyspharm

Laboratory of Systems Pharmacology @ Harvard

Reinventing the fundamental science underlying the development of new medicines and their use in individual patients.

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  1. ashlar ashlar Public

    ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

    Python 166 53

  2. mcmicro mcmicro Public

    Multiple-choice microscopy pipeline

    Nextflow 149 64

  3. scimap scimap Public

    Spatial Single-Cell Analysis Toolkit

    Python 110 36

  4. minerva-story minerva-story Public

    Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

    HTML 56 14

  5. palom palom Public

    Piecewise alignment for layers of mosaics

    Python 43 10

  6. cylinter cylinter Public

    An Interactive Image Segmentation Filter for Multiplex Microscopy

    Python 31 12

Repositories

Showing 10 of 181 repositories
  • okl-analysis Public
    labsyspharm/okl-analysis’s past year of commit activity
    Python 0 1 0 0 Updated Mar 26, 2026
  • 2025-Vallius-Shi-Novikov-melanoma-PCAII Public

    Custom codes for Vallius, Shi, Novikov et al. manuscript 2025

    labsyspharm/2025-Vallius-Shi-Novikov-melanoma-PCAII’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Mar 26, 2026
  • minerva-core-ui Public

    A microscopy viewer for non-experts

    labsyspharm/minerva-core-ui’s past year of commit activity
    TypeScript 1 MIT 3 10 2 Updated Mar 25, 2026
  • minerva-annotation-demo Public
    labsyspharm/minerva-annotation-demo’s past year of commit activity
    JavaScript 0 0 0 0 Updated Mar 25, 2026
  • orion-fish-ms-2026 Public

    Kader_Santagata_ORION-FISH 2026

    labsyspharm/orion-fish-ms-2026’s past year of commit activity
    Python 0 2 0 0 Updated Mar 19, 2026
  • omero-oauth Public Forked from microscopepony/omero-oauth

    OMERO.web application to allow OAuth2 login to OMERO

    labsyspharm/omero-oauth’s past year of commit activity
    Python 1 AGPL-3.0 4 0 0 Updated Mar 18, 2026
  • scimap Public

    Spatial Single-Cell Analysis Toolkit

    labsyspharm/scimap’s past year of commit activity
    Python 110 MIT 36 46 6 Updated Mar 11, 2026
  • mcmicro-lsp Public

    mcmicro helpers for local use within the LSP (especially O2)

    labsyspharm/mcmicro-lsp’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Mar 5, 2026
  • mcmicro Public

    Multiple-choice microscopy pipeline

    labsyspharm/mcmicro’s past year of commit activity
    Nextflow 149 MIT 64 64 2 Updated Feb 27, 2026
  • vae-paper Public
    labsyspharm/vae-paper’s past year of commit activity
    Jupyter Notebook 4 MIT 2 0 0 Updated Feb 21, 2026
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