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@labsyspharm Laboratory of Systems Pharmacology @ Harvard

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    163 repositories

    • okl-analysis

      Public
      Python
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonspatial-analysisimage-analysissingle-cell-analysispypi
      Python
      •
      MIT License
      •31•91•43•2•Updated May 16, 2025May 16, 2025

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
      •
      MIT License
      •15•16•23•1•Updated May 15, 2025May 15, 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 May 15, 2025May 15, 2025

    • harvardtissueatlas

      Public
      Harvard Tissue Atlas website
      SCSS
      •5•3•3•0•Updated May 15, 2025May 15, 2025

    • cycif.org

      Public
      cycif.org GitHub Pages Website
      JavaScript
      •
      MIT License
      •9•2•6•4•Updated May 15, 2025May 15, 2025

    • bftools-docker

      Public
      BioFormats Tools Docker Image
      dockertoolsbio-formats
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •6•24•5•1•Updated May 9, 2025May 9, 2025

    • Eddy

      Public
      The marker localization mapper and mask merger of the quantification folder (MCMICRO)
      Python
      •0•0•0•0•Updated May 9, 2025May 9, 2025

    • ad-personalized

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated May 7, 2025May 7, 2025

    • python-intermediate-may-institute-2025

      Public
      Intermediate Python, data visualization and statistics
      HTML
      •
      Other
      •433•0•2•0•Updated May 1, 2025May 1, 2025

    • ad-rna-editing

      Public
      R
      •1•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • mel-3d-mis

      Public
      MATLAB
      •1•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • CRC_atlas_2022

      Public
      MATLAB
      •
      MIT License
      •4•15•4•0•Updated Apr 8, 2025Apr 8, 2025

    • r-indra-gsea

      Public
      R
      •
      Other
      •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • quantification

      Public
      Quantification module for mcmicro
      Python
      •14•9•7•1•Updated Apr 1, 2025Apr 1, 2025

    • slack-aws-status

      Public
      Slack app for reporting AWS account status
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • PCAII_Atlas_2025

      Public
      project 16 Pre-cancer Atlas second publication data index
      MIT License
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • ome-tiff-pyramid-tools

      Public
      Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.
      Python
      •
      MIT License
      •9•14•0•1•Updated Mar 26, 2025Mar 26, 2025

    • peripheral-neuropathy

      Public
      0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •61•131•63•2•Updated Mar 4, 2025Mar 4, 2025

    • basic-illumination

      Public
      ImageJ BaSiC shading correction for use with Ashlar
      Python
      •
      MIT License
      •9•8•2•0•Updated Mar 4, 2025Mar 4, 2025

    • mcreport

      Public
      Pathology report tool for mcmicro
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •45•141•55•12•Updated Feb 21, 2025Feb 21, 2025

    • omero-oauth

      Public
      OMERO.web application to allow OAuth2 login to OMERO
      Python
      •
      GNU Affero General Public License v3.0
      •4•1•0•0•Updated Feb 13, 2025Feb 13, 2025

    • stic-ms-2024

      Public
      Custom codes related to Kader, Lin, Hug manuscript 2024
      R
      •
      MIT License
      •1•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •12•30•1•1•Updated Jan 31, 2025Jan 31, 2025

    • vae-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jan 31, 2025Jan 31, 2025

    • minerva_analysis

      Public
      JavaScript
      •
      MIT License
      •7•26•22•4•Updated Jan 22, 2025Jan 22, 2025

    • incucyte_stabilizer

      Public
      Python
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025
    0