Repositories list

• zebrahub-multiome-analysis

  Public

  czbiohub-sf/zebrahub-multiome-analysis’s past year of commit activity
  A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•3•0•0•Updated Nov 27, 2025Nov 27, 2025

• ulc-malaria-scope

  Public

  czbiohub-sf/ulc-malaria-scope’s past year of commit activity
  Instrument control software for the Remoscope project.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•5•Updated Nov 25, 2025Nov 25, 2025

• protdata

  Public
  Dataloader for common proteomics search engine outputs into AnnData format

  pythonproteomicsproteomics-datasets+ 1anndata

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•13•0•0•Updated Nov 24, 2025Nov 24, 2025

• biahub

  Public
  HUB for Bio Image Analysis

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•10•65•21•Updated Nov 22, 2025Nov 22, 2025

• protoSpaceJAM

  Public
  CRISPR knock-in design at scale

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•12•10•0•Updated Nov 18, 2025Nov 18, 2025

• iohub

  Public
  Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

  pythonimage-metadatabioimaging+ 3ndimensional-arraysome-zarrome-zarr-converter

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •12•42•45•7•Updated Nov 18, 2025Nov 18, 2025

• Rapid-QC-MS

  Public

  czbiohub-sf/Rapid-QC-MS’s past year of commit activity
  Realtime quality control for mass spectrometry data acquisition

  metabolomicsmass-spectrometryplotly-dash

  Python

  •

  Other

  •2•20•15•0•Updated Nov 17, 2025Nov 17, 2025

• shrimPy

  Public
  shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

  multi-modal-imaginglightsheethigh-throughput-data-analysis+ 2labelfreehigh-throughput-imaging

  Python

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  BSD 3-Clause "New" or "Revised" License

  •5•12•22•7•Updated Nov 14, 2025Nov 14, 2025

• Organelle_IP_analyses_and_figures

  Public

  czbiohub-sf/Organelle_IP_analyses_and_figures’s past year of commit activity
  Jupyter notebooks for analysis and figures related to the native organelle IP paper

  Jupyter Notebook

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  BSD 3-Clause "New" or "Revised" License

  •2•12•1•1•Updated Nov 13, 2025Nov 13, 2025

• python-fish-sorter

  Public

  czbiohub-sf/python-fish-sorter’s past year of commit activity
  Software suite for microscope control with image acquisition and processing tools

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•0•0•Updated Oct 23, 2025Oct 23, 2025

• grassp

  Public
  GRaph-based Analysis of Subcellular/Spatial Proteomics

  spatial-proteomicsscanpyanndata+ 2proteomics-data-analysissubcellular-localization

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•7•0•2•Updated Oct 21, 2025Oct 21, 2025

• 2024-accs-pub

  Public
  Main public repo for the 2024 Automated Cell Culture Splitter publication

  Python

  •0•3•0•0•Updated Sep 29, 2025Sep 29, 2025

• lfm-data-utilities

  Public

  czbiohub-sf/lfm-data-utilities’s past year of commit activity
  A collection of auxiliary data processing tools used in the Remoscope project.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•1•Updated Sep 4, 2025Sep 4, 2025

• compmicro-biautils-env

  Public
  Dockerfile

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  BSD 3-Clause "New" or "Revised" License

  •0•0•3•1•Updated Aug 26, 2025Aug 26, 2025

• tabula-sapiens

  Public

  czbiohub-sf/tabula-sapiens’s past year of commit activity
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

  transcriptomicssingle-cell-rna-seqsapiens+ 3cell-atlascell-ontologieshuman-anatomy

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •9•42•6•2•Updated Aug 21, 2025Aug 21, 2025

• create-sds-app

  Public template
  Repo template for npx create-sds-app

  TypeScript

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  MIT License

  •1•1•0•0•Updated Aug 20, 2025Aug 20, 2025

• CZB--Metadata-Standards

  Public
  Easily-accesible documentation site for CZB's metadata standards efforts

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• compmicro-ndutils-env

  Public
  Shared ndutils environment for maintained by the CompMicro platform

  Dockerfile

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•2•1•Updated Aug 2, 2025Aug 2, 2025

• uxibxx-io-board

  Public
  Simple USB-interfaced I/O boards for lab automation

  C

  •

  Other

  •1•1•0•0•Updated Jul 22, 2025Jul 22, 2025

• napari-iohub

  Public
  OME-Zarr viewer for napari with iohub as the I/O backend

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•7•2•Updated Jul 3, 2025Jul 3, 2025

• ulc-malaria-autofocus

  Public

  czbiohub-sf/ulc-malaria-autofocus’s past year of commit activity
  A single-shot autofocus CNN for the Remoscope project

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• coPylot

  Public
  coPylot - microscope control

  pythoninstrument-control

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11•8•26•16•Updated Jun 12, 2025Jun 12, 2025

• excellxgene

  Public

  czbiohub-sf/excellxgene’s past year of commit activity
  JavaScript

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  MIT License

  •6•13•5•1•Updated Apr 17, 2025Apr 17, 2025

• .github

  Public

  czbiohub-sf/.github’s past year of commit activity
  Organization-level readme and documentation

  0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

• remo-stats-utils

  Public

  czbiohub-sf/remo-stats-utils’s past year of commit activity
  This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.

  machine-learningblooddiagnostics+ 5malariaedge-computinglow-costmalaria-detectionhematology

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Apr 5, 2025Apr 5, 2025

• subcellular-proteomics-curation

  Public

  czbiohub-sf/subcellular-proteomics-curation’s past year of commit activity
  Code and documentation for the curation of proteinxlocation datasets

  Python

  •

  MIT License

  •28•0•0•0•Updated Mar 25, 2025Mar 25, 2025

• reglo-icc-pump-control

  Public
  Python communication driver for Masterflex Ismatec Reglo ICC programmable peristaltic pumps

  Python

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  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Mar 6, 2025Mar 6, 2025

• WellLit

  Public
  Version of WellLit that supports well to well transfers

  Python

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

• WellLit-TubeToWell

  Public

  czbiohub-sf/WellLit-TubeToWell’s past year of commit activity
  Module needed to run Well-Lit in the "Tube to Well" configuration

  Python

  •

  Other

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• WellLit-WelltoWell

  Public
  WelltoWell implementation of the WellLit library

  Jupyter Notebook

  •

  Other

  •1•0•0•0•Updated Feb 14, 2025Feb 14, 2025