shrimPy is a pythonic framework for correlative 3D imaging of physical and molecular properties of cells at high throughput.
In the CZ Biohub Network, 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. We also collaborate closely with the scientific community to support open source tools that are solving the unique analysis needs of researchers.
VisCy is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.
A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics.
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.
dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.
A package that offers a comprehensive pipeline, command line interface, and napari plugin for quantitative label-free microscopy.
Software to measure intrinsic order with wave optical reconstructions of density and anisotropy.
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.