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    13 repositories

    • starfish

      Public
      starfish: unified pipelines for image-based transcriptomics
      pythontranscriptomicsimaginghuman-cell-atlas
      Python
      •
      MIT License
      •70•243•160•15•Updated Nov 20, 2025Nov 20, 2025

    • spacetx.github.io

      Public
      SpaceTx website
      Jupyter Notebook
      •0•0•0•0•Updated Jun 14, 2023Jun 14, 2023

    • spacetx-hca-flattener

      Public
      Python
      •
      MIT License
      •0•0•0•2•Updated Dec 26, 2022Dec 26, 2022

    • spacetx-biohub-writer

      Public
      Conversion tool from biohub's DB format to spacetx format
      Python
      •
      MIT License
      •1•0•0•1•Updated Nov 15, 2021Nov 15, 2021

    • spacetx-research

      Public
      Contains research projects related to image-based transcriptomics assays
      Jupyter Notebook
      •0•5•22•4•Updated May 26, 2021May 26, 2021

    • slicedimage

      Public
      Python
      •
      MIT License
      •3•7•8•0•Updated May 26, 2020May 26, 2020

    • starfish-workflows

      Public
      Solutions for running at-scale workflows with starfish
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 15, 2019Nov 15, 2019

    • starfish-analysis

      Public
      Contains analyses executed using the starfish package
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 3, 2019Jun 3, 2019

    • spacetx-writer

      Public
      Convert supported filesets to the SpaceTx format
      conversionbio-formatstranscriptomicsimagingomefile-formatshuman-cell-atlas
      Java
      •
      GNU General Public License v2.0
      •1•3•6•0•Updated Apr 24, 2019Apr 24, 2019

    • segment_and_map

      Public
      This repo includes scripts for segmenting spacetx data sets and mapping the results to a reference RNA-seq data set.
      HTML
      •
      Other
      •0•2•0•0•Updated Apr 11, 2019Apr 11, 2019

    • upload-validator

      Public
      HumanCellAtlas upload-service validator for SpaceTx files
      dockervalidatortranscriptomicsimaginghuman-cell-atlas
      Makefile
      •0•0•0•0•Updated Mar 5, 2019Mar 5, 2019

    • sptx-format

      Public archive
      Image data format specification for spaceTx
      Python
      •
      MIT License
      •2•4•1•2•Updated Sep 5, 2018Sep 5, 2018

    • starfish-viz

      Public
      A web-based visualization for image based transcriptomics data
      JavaScript
      •
      MIT License
      •0•0•1•0•Updated Aug 10, 2018Aug 10, 2018