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    52 repositories

    • OTTR

      Public
      Organotypic Timelapse recording with Transcriptomic Readout (OTTR) links cell identity to cell behaviour in human tissues
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • fetal_brain_multiomics

      Public
      Supplementary files and notebooks to recreate figures.
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•17•0•0•Updated Aug 12, 2025Aug 12, 2025

    • human-meninges-development

      Public
      Supplementary code and data to our study of the developing human meninges by Vinsland et al. (manuscript in preparation).
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Jul 18, 2025Jul 18, 2025

    • oligopy

      Public
      Python
      •2•2•0•1•Updated Jul 9, 2025Jul 9, 2025

    • adult-human-brain

      Public
      Cytograph version used for adult human-brain analysis
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •20•89•11•0•Updated Jun 16, 2025Jun 16, 2025

    • FISHscale

      Public
      Spatial analysis of FISH data
      Jupyter Notebook
      •9•31•5•0•Updated May 20, 2025May 20, 2025

    • glioblastoma_wound_response

      Public
      Repository for Glioblastoma EEL-FISH data and code
      Jupyter Notebook
      •0•5•0•0•Updated Apr 25, 2025Apr 25, 2025

    • FISHspace

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • loom-viewer

      Public
      Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •6•36•44•1•Updated Jan 10, 2025Jan 10, 2025

    • loompy

      Public
      Python implementation of the Loom file format - http://loompy.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •37•146•38•2•Updated Dec 16, 2024Dec 16, 2024

    • developing-human-brain

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•35•13•0•Updated Aug 15, 2024Aug 15, 2024

    • shoji

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•6•1•0•Updated May 28, 2024May 28, 2024

    • chromograph

      Public
      Camiel's scATAC-seq analysis pipeline
      Python
      •1•12•1•0•Updated Apr 15, 2024Apr 15, 2024

    • pysmFISH_auto

      Public
      Version of the pysmFISH pipeline that run without human in the loop
      Jupyter Notebook
      •
      MIT License
      •4•6•0•0•Updated Mar 29, 2024Mar 29, 2024

    • cytograph-shoji

      Public
      Jupyter Notebook
      •0•4•1•0•Updated Mar 17, 2024Mar 17, 2024

    • MXII-valve

      Public
      MX Series II actuated valve
      Python
      •
      MIT License
      •0•7•0•0•Updated Feb 21, 2024Feb 21, 2024

    • cytograph-dev

      Public
      Algorithms for analysis of very large single-cell RNA-seq datasets
      Jupyter Notebook
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • STspace

      Public
      A novel machine learning pipeline to analyse spatial transcriptomics data
      Python
      •
      Other
      •28•0•0•0•Updated Jun 18, 2023Jun 18, 2023

    • auto-annotation

      Public
      Computer-readable annotation for cell types and states
      0•1•2•0•Updated Jun 13, 2023Jun 13, 2023

    • cytograph2

      Public
      Python
      •0•15•1•0•Updated Feb 21, 2023Feb 21, 2023

    • Py_TC-720

      Public
      Python library to control the TC-720 temperature controller
      Python
      •
      MIT License
      •8•2•1•0•Updated Jan 30, 2023Jan 30, 2023

    • flamemaps

      Public
      Demo page for flame maps
      JavaScript
      •0•2•4•16•Updated Dec 7, 2022Dec 7, 2022

    • auto-annotation-ah

      Public
      Auto-annotations for analysis of the adult human brain
      2•6•1•0•Updated Sep 28, 2022Sep 28, 2022

    • ROBOFISH

      Public
      Control and installation of a cyclic smFISH robot
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 10, 2022Aug 10, 2022

    • BoneFight

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•8•0•0•Updated Nov 1, 2021Nov 1, 2021

    • tecancavro

      Public
      Python package to control Tecan Cavro OEM syringe pumps
      JavaScript
      •
      Other
      •20•0•0•0•Updated Oct 16, 2021Oct 16, 2021

    • Oasis_chiller

      Public
      Python library to control the Solid State Oasis recirculating chillers for temperature control.
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 16, 2021Oct 16, 2021

    • ThermoCube

      Public
      Python library for control of the Solid State ThermoCube recirculating chiller.
      Python
      •
      MIT License
      •1•2•0•0•Updated Oct 16, 2021Oct 16, 2021

    • cytograph

      Public
      Algorithms for single-cell analysis
      Python
      •5•29•1•0•Updated Jul 19, 2021Jul 19, 2021

    • auto-annotation-md

      Public
      Auto-annotations from Mouse brain development
      6•13•2•1•Updated Jul 11, 2020Jul 11, 2020