Tools

In the CZ Biohub Network, we know that open access to tools, data, and other resources accelerates scientific progress. Not only do we invent tools to open new avenues for biomedical research, but we make them easily available for researchers worldwide to access and use. We also collaborate closely with the scientific community to support open-source tools that help solve the unique problems of biomedical data analysis. The CZ Biohub Network is a group of nonprofit research institutes created and supported by the Chan Zuckerberg Initiative.

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protoSpaceJAM

protoSpaceJAM is an all-around platform for CRISPR knock-in design at scale.

Access the webapp Download the tool

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cryoET Data Portal

The cryoET Data Portal is a cloud-based, open-source portal aimed at driving the development of automated annotations of cryoET datasets. This tool has the potential to shorten data processing time from months or years to weeks.

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shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.

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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.

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VisCy is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.

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Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells.

Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.

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OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.

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

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Rapid QC-MS

Rapid QC-MS is an all-in-one solution for automated quality control of liquid chromatography-mass spectrometry instrument runs, both during and after data acquisition.

download the tool access the user guide

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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.

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Rapid Response resources

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.

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Tabula Muris Senis

A comprehensive compendium of single-cell transcriptomic data from the model organism Mus musculus.

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A compendium of single-cell transcriptome data from the mouse.

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COVID Tissue Atlas

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.

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Self-supervised models for encoding protein localization patterns from microscopy images.

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MERFISH mouse dataset

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.

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dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.

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A package that offers a comprehensive pipeline, command line interface, and napari plugin for quantitative label-free microscopy.

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Software to measure intrinsic order with wave optical reconstructions of density and anisotropy.

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Aydin: User-friendly, feature-rich, fast image denoising tool for all

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.

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Human Lung Cell Atlas

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.

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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.

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DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments.

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Metagenomic sequencing: Introduction and lab setup

Part 1 of the Metagenomic Sequencing training from the Rapid Response Team.

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Metagenomic sequencing: Study design and sample preparation

Part 2 of the Metagenomic Sequencing training from the Rapid Response Team. Provides overview of study design and best practices for xNA extraction.

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Metagenomic sequencing: Introduction to Illumina sequencing and data analysis for mNGS using IDseq

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.

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Metagenomic sequencing: Library preparation for mNGS

Part 4 of the Metagenomic Sequencing training from the Rapid Response Team. In-depth guide on the process of library preparation.

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Metagenomic sequencing: Loading the sequencer – iSeq loading guide

Part 5 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide on loading the iSeq 100.

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Metagenomic sequencing: Loading the sequencer – MiSeq loading guide

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.

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Enrichment/depletion methods for sequencing: FLASH protocol

Finding Low Abundance Sequences by Hybridization (FLASH) Protocol developed at CZ Biohub.

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Enrichment/depletion methods for sequencing: FLASH publication

Official publication of the Finding Low Abundance Sequences by Hybridization (FLASH) protocol developed at CZ Biohub.

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How to make your own SPRI beads

Overview and training guide on homemade Solid Phase Reverse Immobilization (SPRI) beads.

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Sequencing SARS-CoV-2 for public health laboratories

CZ Biohub Rapid Response Team's handbook for public health labs on sequencing SARS-CoV2.

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Scaling sequencing

Instructions from CZ Biohub Rapid Response team on increasing sample throughput for sequencing, levels of scaling, and equipment options for each level.

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Metagenomic next-generation sequencing (mNGS) protocol

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.

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SARS-CoV-2 ARTIC sequencing using Illumina; library prep protocol V.4

Most up-to-date version of the protocol for experiment investigating the effect of fragmentation time on the genome recovery of SARS-CoV-2 from COVID-19-positive patient samples.

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