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    • PySeq2500

      Public
      Control an Illumina HiSeq 2500 System
      Python
      MIT License
      112106Updated Apr 27, 2026Apr 27, 2026
    • Python
      GNU General Public License v3.0
      0030Updated Apr 20, 2026Apr 20, 2026
    • Approximate Bayesian inference of spatial cellular gene expression conditioned on covariates of interest
      Python
      0000Updated Apr 8, 2026Apr 8, 2026
    • Workflow for reproducing main figures and results from SPACE-Tag manuscript
      Jupyter Notebook
      MIT License
      0000Updated Apr 2, 2026Apr 2, 2026
    • hudson

      Public
      Pyseq 4i spatial pipeline
      Python
      GNU General Public License v3.0
      2241Updated 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.
      0000Updated Mar 11, 2026Mar 11, 2026
    • Snakemake workflow for preprocessing of SPACE-Tag raw data for downstream analysis
      Jupyter Notebook
      Other
      0000Updated Mar 9, 2026Mar 9, 2026
    • Python
      0000Updated Dec 29, 2025Dec 29, 2025
    • .github

      Public
      0000Updated Nov 23, 2025Nov 23, 2025
    • INLAomics

      Public
      Bayesian Hierchical models for multiomic spatial transcriptomics using INLA
      HTML
      MIT License
      0100Updated Oct 20, 2025Oct 20, 2025
    • shmseq

      Public
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      0900Updated Feb 3, 2024Feb 3, 2024
    • PICASSO

      Public
      Development of PICASSO plugin for napari
      Jupyter Notebook
      GNU General Public License v3.0
      31630Updated Jan 17, 2023Jan 17, 2023
    • Code for the Kedmi et al paper
      Jupyter Notebook
      0010Updated 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
      4000Updated May 2, 2022May 2, 2022
    • Svelte
      GNU General Public License v2.0
      2000Updated Apr 14, 2022Apr 14, 2022
    • Python
      MIT License
      0100Updated Sep 25, 2019Sep 25, 2019
    • A collection of microscope hardware interfaces in various languages and implementations.
      Python
      2000Updated Jan 18, 2019Jan 18, 2019
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