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    18 repositories

    • napari-histo

      Public
      Napari plugin allowing the user to edit pixel-level labels of histology images. Useful for refining semantic segmentation maps of tissue types or cell segments …
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • abcSplotch

      Public
      Approximate Bayesian inference of spatial gene expression at cellular resolution, disentangling cell- or sample covariate-driven variation from tissue-specific …
      transcriptomicsspatial-data-analysisgeneralized-linear-models
      transcriptomicsspatial-data-analysisgeneralized-linear-modelssingle-cell-rna-seqapproximate-bayesian-inferencespatial-transcriptomicsspatial-data-integration
      Python
      •0•1•0•0•Updated Jul 29, 2026Jul 29, 2026

    • pyseq-image

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Jun 17, 2026Jun 17, 2026

    • PySeq2500

      Public
      Control an Illumina HiSeq 2500 System
      Python
      •
      MIT License
      •11•21•0•6•Updated May 21, 2026May 21, 2026

    • SPACE-Tag-reproducibility

      Public
      Workflow for reproducing main figures and results from SPACE-Tag manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • hudson

      Public
      Pyseq 4i spatial pipeline
      Python
      •
      GNU General Public License v3.0
      •2•2•4•1•Updated Mar 25, 2026Mar 25, 2026

    • SPACE-Tag

      Public
      Links to repos for preprocessing of SPACE-Tag datasets and reproducing figures from the SPACE-Tag manuscript.
      0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • SPACE-Tag-preprocessing

      Public
      Snakemake workflow for preprocessing of SPACE-Tag raw data for downstream analysis
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • celery-pipeline

      Public
      Python
      •0•0•0•0•Updated Dec 29, 2025Dec 29, 2025

    • .github

      Public
      0•0•0•0•Updated Nov 23, 2025Nov 23, 2025

    • INLAomics

      Public
      Bayesian Hierchical models for multiomic spatial transcriptomics using INLA
      HTML
      •
      MIT License
      •0•1•0•0•Updated Oct 20, 2025Oct 20, 2025

    • shmseq

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•9•0•0•Updated Feb 3, 2024Feb 3, 2024

    • PICASSO

      Public
      Development of PICASSO plugin for napari
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•16•3•0•Updated Jan 17, 2023Jan 17, 2023

    • Kedmi-CITEseq

      Public
      Code for the Kedmi et al paper
      Jupyter Notebook
      •0•0•1•0•Updated Aug 15, 2022Aug 15, 2022

    • pyseq2501

      Public
      Use the Illumina HiSeq 2000/2500 as an epifluorescence microscope with fluidics control.
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated May 2, 2022May 2, 2022

    • pyseq2501-web

      Public
      Svelte
      •
      GNU General Public License v2.0
      •2•0•0•0•Updated Apr 14, 2022Apr 14, 2022

    • PySeq2500-OLD

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 25, 2019Sep 25, 2019

    • microscope-interfaces

      Public
      A collection of microscope hardware interfaces in various languages and implementations.
      Python
      •2•0•0•0•Updated Jan 18, 2019Jan 18, 2019
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