shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.
In the CZ Biohub Network, we know that open access to tools, data, and other resources expedites solutions. Not only do we invent tools to enable avenues for biomedical research that were not possible before, but we also make them available for the scientific community to access and use. We also collaborate closely with the scientific community to support open source tools that are solving the unique analysis needs of researchers.
VisCy is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.
Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.
OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.
A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics.
An interactive data explorer for single-cell datasets that leverages modern web development techniques to enable fast visualizations of at least 1 million cells, enabling data exploration.
CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
napari is a community-built, Python-based, open source tool designed for browsing, annotating, and analyzing large multi-dimensional images. The CZ Biohub and the Chan Zuckerberg Initiative (CZI) collaborate with napari, and CZI built the napari hub to help users find plugins to solve their analysis needs.
mNGS protocols and training materials that were developed in collaboration with the Genomics and Sequencing Platform at CZ Biohub and the CZ ID team at the Chan Zuckerberg Initiative.
A new single-objective design that is capable of imaging large samples, with a large imaging volume, uncompromised image resolution and speed, and multi-view imaging.
A comprehensive compendium of single-cell transcriptomic data from the model organism Mus musculus.
Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells.
The COVID Tissue Atlas enables the investigation of both cell type-specific and cross-organ transcriptional responses to COVID-19, providing insights into the molecular networks affected by the disease and highlighting novel potential targets for therapies and drug development.
Self-supervised models for encoding protein localization patterns from microscopy images.
A comparative study, in collaboration with Vizgen, Inc. and UC San Francisco, of MERFISH spatial transcriptomics in mouse liver and kidney with bulk and single-cell RNA sequencing data from Tabula Muris Senis.
dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.
A package that offers a comprehensive pipeline, command line interface, and napari plugin for quantitative label-free microscopy.
Software to measure intrinsic order with wave optical reconstructions of density and anisotropy.
Aydin is a user-friendly, feature-rich, and fast image denoising tool that provides a number of self-supervised, auto-tuned, and unsupervised image denoising algorithms.
Provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.
The Fly Cell Atlas brings together Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics, to build comprehensive cell atlases during different developmental stages and disease models.
Secure, cloud-based platform with no-code genomic epidemiology analysis platform for public health.
DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments.
CrispyCrunch is a tool for defining batches of CRISPR edits and analyzing their basic effects.
Part 1 of the Metagenomic Sequencing training from the Rapid Response Team.
Part 2 of the Metagenomic Sequencing training from the Rapid Response Team. Provides overview of study design and best practices for xNA extraction.
Part 3 of the Metagenomic Sequencing training from the Rapid Response Team. Provides an introduction to Illumina and an overview of library prep, sequencing, data analysis, and Pathogen ID.
Part 4 of the Metagenomic Sequencing training from the Rapid Response Team. In-depth guide on the process of library preparation.
Part 5 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide on loading the iSeq 100.
Part 6 of 6 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide to setting up and loading the Illumina MiSeq.
Finding Low Abundance Sequences by Hybridization (FLASH) Protocol developed at CZ Biohub.
Official publication of the Finding Low Abundance Sequences by Hybridization (FLASH) protocol developed at CZ Biohub.
Overview and training guide on homemade Solid Phase Reverse Immobilization (SPRI) beads.
CZ Biohub Rapid Response Team's handbook for public health labs on sequencing SARS-CoV2.
Instructions from CZ Biohub Rapid Response team on increasing sample throughput for sequencing, levels of scaling, and equipment options for each level.
A centralized location for protocols used for the mNGS training for the Gates Grand Challenges Explorations Grants. Contains guidelines for best practices that are subject to change.