Tools & Resources
At Biohub, 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 partners on innovative scientific solutions and with the scientific community to support open-source tools that help solve the unique problems of biomedical data analysis.
Organelle Profiling
Global organelle profiling reveals the human proteome’s subcellular landscape and its dynamic remodeling
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.
Tabula Sapiens
Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells.
ZebraHub
Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.
OpenCell
OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.
CELL×GENE
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
CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
Tabula Muris
A compendium of single-cell transcriptome data from the mouse.
Tabula Muris Senis
A comprehensive compendium of single-cell transcriptomic data from the model organism Mus musculus.
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.
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.
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.
Fly Cell Atlas
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.
shrimPy
shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.
DaXi
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.
AreTomo2
AreTomo2, a multi-GPU accelerated software package, enables real-time assessment of imaging sample quality and the adjustment of collection parameters as needed. This provides researchers with a new opportunity to assess and increase their sample quality in real-time.
GCtfFind
GCtfFind is a new application that robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.
MotionCor3
MotionCor3 is a multi-GPU accelerated program that corrects anisotropic beam-induced sample motion at the single pixel level, suitable for both single particle and tomographic images. MotionCor3 enables motion-corrected images that keep pace with data collection.
protoSpaceJAM
Global organelle profiling reveals the human proteome’s subcellular landscape and its dynamic remodeling
shrimPy
shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.
VisCy
VisCy is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.
PoMeLo
A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics.
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.
dexp
dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.
WaveOrder
WaveOrder is a physics-informed, predictive model that unifies forward and inverse wave-optics to reconstruct phase, absorption, birefringence, diattenuation, and fluorescence density/orientation from multi-contrast microscopy, with machine learning auto-tuning for shift-variant blind deconvolution.
Aydin
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.
DASHit
DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments.
Delmic
Delmic is a passionate high-tech company that develops powerful and user-friendly solutions for electron microscopy, bringing life science and material science researchers and organizations closer to research insights across diverse application fields.
Thermo Fisher Scientific
Whether they are improving life for patients, protecting our global climate or keeping people safe, our customers look to Thermo Fisher Scientific for innovative solutions. Products and services sold under the following Thermo Fisher brands enable customers to push science and technology a step beyond.
Zeiss
For over 175 years, leading scientists and industrial customers have trusted ZEISS microscopy solutions and software to transform questions into discoveries that shape the future.
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.
cytoself
Self-supervised models for encoding protein localization patterns from microscopy images.
Metagenomic sequencing: Introduction and lab setup
Part 1 of the Metagenomic Sequencing training from the Rapid Response Team.
Metagenomic sequencing: Study design and sample prep
Part 2 of the Metagenomic Sequencing training from the Rapid Response Team. Provides overview of study design and best practices for xNA extraction.
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.
Metagenomic sequencing: Library prep for mNGS
Part 4 of the Metagenomic Sequencing training from the Rapid Response Team. In-depth guide on the process of library preparation.
Metagenomic sequencing: Loading the iSeq sequencer
Part 5 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide on loading the iSeq 100.
Metagenomic sequencing: Loading the MiSeq sequencer
Part 6 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide to setting up and loading the Illumina MiSeq.
Enrichment/depletion methods for sequencing: FLASH protocol
Finding Low Abundance Sequences by Hybridization (FLASH) Protocol developed at Biohub.
Enrichment/depletion methods for sequencing: FLASH publication
Official publication of the Finding Low Abundance Sequences by Hybridization (FLASH) protocol developed at Biohub.
How to make your own SPRI beads
Overview and training guide on homemade Solid Phase Reverse Immobilization (SPRI) beads.
Sequencing SARS-CoV-2 for public health laboratories
Biohub Rapid Response Team’s handbook for public health labs on sequencing SARS-CoV2.
Scaling sequencing
Instructions from Biohub Rapid Response team on increasing sample throughput for sequencing, levels of scaling, and equipment options for each level.
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.
SARS-CoV-2 ARTIC sequencing using Illumina library prep protocol v4
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.