Chan Zuckerberg Biohub San Francisco

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

Dataloader for common proteomics search engine outputs into AnnData format

Jupyter notebooks for analysis and figures related to the native organelle IP paper

HUB for Bio Image Analysis

Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.

GRaph-based Analysis of Subcellular/Spatial Proteomics

A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics

A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)

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

Software suite for microscope control with image acquisition and processing tools

Main public repo for the 2024 Automated Cell Culture Splitter publication

Comparison of single-cell RNA Velocity methods in developmental contexts

A repository for notebooks, figures, and utilities for cell-type annotation tutorial manuscript using CZ CELLxGENE ecosystem

MAGeCK analysis automated by Nextflow

Public repo for the Automated Cell Culture Splitter protocol framework and tools

Simple USB-interfaced I/O boards for lab automation

Simple standalone command-line tool and Python library for controlling an Opentrons Temperature Module ("Tempdeck"). Not affiliated with Opentrons.

Python libraries for automating cell sorting with the Sony SH800S GUI.

Python communication driver for Masterflex Ismatec Reglo ICC programmable peristaltic pumps

Webserver allowing non-bioinformaticians to easily run protospaceJAM.

Build a Napari image with common plugins

This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.

A collection of auxiliary data processing tools used in the Remoscope project.

Shared ndutils environment for maintained by the CompMicro platform

Public repo for software that drives the ACCS Cell Counting Imager

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

Organization-level readme and documentation