Our Work - CZ Biohub San Francisco

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groups-projects--hero"> <figure class="abs-full"> <img class="block img-fit-cover " src="https://www.czbiohub.org/sf/wp-content/uploads/sites/18/2023/09/our-work-highlight-hero-1.jpg" alt=""> </figure> <div class="groups-projects--hero-content "> <div class="sub-wrap"> <p class="eye--l">OUR WORK</p> </div> <h1>We create, collaborate, catalyze</h1> <div class="copy"> <p>We create and openly disseminate knowledge and technologies through collaborative, interdisciplinary research to catalyze science</p> </div> </div> </section> <section class="owh--intro"> <div class="owh--intro-title"> <h2>Cells are the fundamental unit of life. Our goal is to understand dynamic cell systems across scales, in both healthy and diseased states.</h2> </div> <div class="owh--intro-row flex wrap"> <div class="col"> <p>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.</p> <p>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.</p> <p>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. We also partner with institutes across the CZ Biohub Network, created and supported by the <a href="https://chanzuckerberg.com/" target="_blank" rel="noopener">Chan Zuckerberg Initiative</a>.</p> </div> <div class="col"> <img src="https://www.czbiohub.org/sf/wp-content/uploads/sites/18/2023/09/Group-8173.png" alt=""> </div> </div> </section> <section class="owh--highlight"> <div class="container"> <div class="owh--highlight-wrap"> <a class="owh--highlight-block right" href="https://www.czbiohub.org/sf/research-groups/" target=""> <figure class="bg"> <img src="https://www.czbiohub.org/sf/wp-content/uploads/sites/18/2023/09/Rectangle-2960.jpg" alt="Mapping dynamic cell systems across scales image"> </figure> <div class="copy"> <h2>RESEARCH GROUPS</h2> <h3>Mapping dynamic cell systems across scales</h3> <p>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.</p> <div class="btn desktop">Learn more</div> <div class="link-wrap mobile"> <svg width="19" height="19" viewBox="0 0 19 19" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M9.79395 16.3403C13.5219 16.3403 16.5439 13.3183 16.5439 9.59035C16.5439 5.86243 13.5219 2.84035 9.79395 2.84035C6.06602 2.84035 3.04395 5.86243 3.04395 9.59035C3.04395 13.3183 6.06602 16.3403 9.79395 16.3403Z" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.79395 6.21535V12.9653" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.1689 9.59035H6.41895" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> </svg> <span>Learn more</span> </div> </div> </a> </div> <div class="owh--highlight-wrap"> <a class="owh--highlight-block" href="https://www.czbiohub.org/sf/technology-platforms/" target=""> <figure class="bg"> <img src="https://www.czbiohub.org/sf/wp-content/uploads/sites/18/2023/09/Rectangle-2959.jpg" alt="Doesn’t exist?</br>We’ll build it. image"> </figure> <div class="copy"> <h2>Technology Platforms</h2> <h3>Doesn’t exist?</br>We’ll build it.</h3> <p>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.</p> <div class="btn desktop">Learn more</div> <div class="link-wrap mobile"> <svg width="19" height="19" viewBox="0 0 19 19" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M9.79395 16.3403C13.5219 16.3403 16.5439 13.3183 16.5439 9.59035C16.5439 5.86243 13.5219 2.84035 9.79395 2.84035C6.06602 2.84035 3.04395 5.86243 3.04395 9.59035C3.04395 13.3183 6.06602 16.3403 9.79395 16.3403Z" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.79395 6.21535V12.9653" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.1689 9.59035H6.41895" stroke="#00A3E0" stroke-width="1.10334" stroke-linecap="round" stroke-linejoin="round"/> </svg> <span>Learn more</span> </div> </div> </a> </div> </div> </section> <section class="owh--team"> <figure class="bg"> <img src="https://www.czbiohub.org/sf/wp-content/uploads/sites/18/2023/09/biohubbbin-teamphoto.jpg" alt=""> </figure> <div class="copy"> <h2>INVESTIGATOR PROGRAM</h2> <h3>Building community to catalyze innovation</h3> <p>The Investigator Program at CZ Biohub SF is funding research by world-renowned scientists, engineers, and technologists from Stanford University, UC Berkeley, and UCSF.</p> <a href="https://www.czbiohub.org/sf/investigator-program/" target="" class="btn">Learn more</a> </div> </section>  <section class="locationsHome__tools"> <div class="container-1060 relative"> <div class="locationsHome__sec-title"> <h2 class="eye--l text-uppercase"> Featured Tools & Projects </h2> </div> <div class="locationsHome__tools__list"> <div class="resources__grid-item"> <a href="https://github.com/czbiohub-sf/shrimPy" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2023/12/shrimPy.png" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> shrimPy </span> <p class="p--s">shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://github.com/royerlab/daxi" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2022/01/daxi-1.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> DaXi </span> <p class="p--s">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.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://github.com/mehta-lab/viscy" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2023/12/VisCy.png" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> VisCy </span> <p class="p--s">VisCy is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://tabula-sapiens-portal.ds.czbiohub.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/tabula-sapiens.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> Tabula Sapiens </span> <p class="p--s">Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://zebrahub.ds.czbiohub.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2022/08/Zebrahub-logo.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> Zebrahub </span> <p class="p--s">Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://opencell.czbiohub.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/opencell_logo_v3.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> OpenCell </span> <p class="p--s">OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://github.com/czbiohub-sf/pomelo" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2023/08/pomelo-v2.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> PoMeLo </span> <p class="p--s">A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://cellxgene.cziscience.com/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/cellxgene.png" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> CZ CELLxGENE </span> <p class="p--s">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.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://czid.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/czid-logo-1.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> CZ ID </span> <p class="p--s">CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://www.napari-hub.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/napari-logo.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> napari </span> <p class="p--s">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. </p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://www.czbiohub.org/rapid-response/resources/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2023/02/hero-resources.jpeg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> Rapid Response </span> <p class="p--s">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.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="https://tabula-muris-senis.ds.czbiohub.org/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/tabula-senis.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> Tabula Muris Senis </span> <p class="p--s">A comprehensive compendium of single-cell transcriptomic data from the model organism Mus musculus.</p> </article> <div class="resources__grid-item-actions"> <span class="item"> <svg width="16" height="16" viewBox="0 0 16 16" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.60258 13.3045C10.7517 13.3045 13.3045 10.7517 13.3045 7.60258C13.3045 4.45348 10.7517 1.90063 7.60258 1.90063C4.45348 1.90063 1.90063 4.45348 1.90063 7.60258C1.90063 10.7517 4.45348 13.3045 7.60258 13.3045Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.60254 4.75159V10.4535" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M10.4537 7.60254H4.75171" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> Learn More </span> </div> </div> </div> </a> </div> <div class="resources__grid-item"> <a href="/sf/tabula-muris/" target="_blank"> <div class="resources__grid-item-content"> <div class="inner-wrap"> <figure> <img src="https://www.czbiohub.org/wp-content/uploads/2021/05/tabula-muris.jpg" alt="Thumbnail"> </figure> <article> <span class="title p--large-strong"> Tabula Muris </span> <p class="p--s">A compendium of single-cell transcriptome data from the mouse.</p> </article> <div 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