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Tools

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.

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shrimPy

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

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VisCy

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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PoMeLo

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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napari

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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dexp

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

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recOrder

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

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WaveOrder

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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DASHit

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

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