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.
CZ Biohub Resources
At CZ Biohub, 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.
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.
Secure, cloud-based platform with no-code genomic epidemiology analysis platform for public health.
CrispyCrunch is a tool for defining batches of CRISPR edits and analyzing their basic effects.
CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments
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
dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.
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.
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.
Overview and training guide on homemade Solid Phase Reverse Immobilization (SPRI) beads.
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.
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.
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.
Software that allows the user to design, train, and evaluate U-Net models using YAML config files
napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images.
OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.
A package that offers a comprehensive pipeline, command line interface, and napari plugin for quantitative label-free microscopy.
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.
Instructions from CZ Biohub Rapid Response team on increasing sample throughput for sequencing, levels of scaling, and equipment options for each level.
CZ Biohub Rapid Response Team's handbook for public health labs on sequencing SARS-CoV2.
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.
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.