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Howard Hughes Medical Institute

@JaneliaSciComp

GitHub organization maintained by Scientific Computing Software at HHMI's Janelia Research Campus for use by HHMI staff and external collaborators.

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  1. Tools for distributed alignment of massive images

    Jupyter Notebook 95 24

  2. ImgLib2/BDV implementation of Stitching for large datasets

    Java 80 17

  3. EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 36 13

  5. Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

    Java 33 25

  6. Running compute-intense parts of BigStitcher distributed

    Java 30 19

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Showing 10 of 325 repositories

  • JaneliaSciComp/workstation’s past year of commit activity

    Java

    28 12 1 6

    Updated Jun 22, 2026

  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity

    TypeScript

    26

    BSD-3-Clause

    4 2 7

    Updated Jun 21, 2026

  • x2s3 Public

    S3 Proxy Service

    JaneliaSciComp/x2s3’s past year of commit activity

    Python

    13

    BSD-3-Clause

    1 1 0

    Updated Jun 21, 2026

  • BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    JaneliaSciComp/BigStitcher’s past year of commit activity

    Java

    80

    GPL-2.0

    17 91 2

    Updated Jun 21, 2026

  • JaneliaSciComp/fileglancer-docs’s past year of commit activity

    MDX 0 BSD-3-Clause 0

    0 1

    Updated Jun 20, 2026

  • runnables Public

    Schema for manifests defining runnable tasks

    JaneliaSciComp/runnables’s past year of commit activity

    Python 0 BSD-3-Clause 0

    0 0

    Updated Jun 20, 2026

  • JaneliaSciComp/easifish’s past year of commit activity

    Nextflow

    1

    BSD-3-Clause

    1 1 0

    Updated Jun 19, 2026

  • JaneliaSciComp/nextflow-modules’s past year of commit activity

    Nextflow

    1

    BSD-3-Clause 0

    0 0

    Updated Jun 19, 2026

  • doi_common Public

    Library of common DOI-related functions for Python

    JaneliaSciComp/doi_common’s past year of commit activity

    Python 0 BSD-3-Clause 0

    0 0

    Updated Jun 19, 2026

  • multiview-reconstruction Public

    Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

    JaneliaSciComp/multiview-reconstruction’s past year of commit activity

    Java

    33

    GPL-2.0

    25 30 6

    Updated Jun 19, 2026

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