shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.
We create, collaborate, catalyze
We create and openly disseminate knowledge and technologies through collaborative, interdisciplinary research to catalyze science
Cells are the fundamental unit of life. Our goal is to understand dynamic cell systems across scales, in both healthy and diseased states.
We study cell physiology across scales: at the molecular level of transcriptomes, proteomes, and metabolomes; at the whole-cell level of functionally and compositionally distinct organelles; and at the whole-organism level of divergent cell types and changing cell states. And at the population level we collaborate with scientists in low- and middle-income countries, building capacity in state-of-the-art metagenomics and molecular epidemiology to detect and manage infectious diseases.
We develop new technologies for high-throughput, scalable cell and molecular biology; genomics; transcriptomics; customized and automated microscopy; mass spectrometry; and AI and data analytics.
And we build scientific bridges with our partner universities – Stanford University, UC Berkeley, and UCSF – through our Investigator Program, creating and catalyzing connections and a rich culture of scientific exchange.
Mapping dynamic cell systems across scales
Scientists still have much to learn about how cells function. In order to understand the mechanisms of disease and develop technologies that will lead to actionable diagnostics and effective therapies, we study cell physiology across scales.
Doesn’t exist?We’ll build it.
Access to data and tools expedites solutions and catalyzes innovation. Our Technology Platforms proactively identify and develop enabling technologies that advance biomedical research at CZ Biohub SF, our partner universities, and worldwide through its open-source dissemination policy. If it doesn’t exist, we will build it.
Building community to catalyze innovation
The Investigator Program at CZ Biohub SF is funding research by world-renowned scientists, engineers, and technologists from Stanford University, UC Berkeley, and UCSF.Learn more
Featured Tools & Projects
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.