CZI Imaging Tools: napari

Napari: A Multi-Dimensional Image Viewer for Python

A video of the napari visualization interface, browsing and segmenting cells infected with SARS-CoV-2 virus from a high-throughput screen. Data from Recursion Pharmaceuticals.

Napari is an interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large images — providing GUI access to a plugin ecosystem of image analysis tools for scientists to use in their daily work. Napari was designed to help Python practitioners as well as biologists and other scientists who want to access Python’s enormous scientific ecosystem, but may not have prior coding experience. 

As an open source tool, napari is built on inclusive, community-driven, and collaborative values and aims to serve scientific applications focused on visualization with simple, readable implementations. Researchers used napari to view SARS-CoV-2 virus particles after first converting the images to Zarr  — an open source tool funded by CZI’s Essential Open Source Software for Science program.   

Napari supports large data sets and has six main distinct layer types that each correspond to a different data type, visualization, and interactivity. Users can add multiple layers of different types into the viewer and then work to adjust their properties, including performing manual annotations by painting labels or drawing polygons. All layer types support n-dimensional data, and the viewer allows users to quickly browse and visualize either 2D or 3D slices of these data.

Napari is a collaboration across CZI, CZI grantees, the Chan Zuckerberg Biohub, and many other scientists and computational biologists who have contributed to its growth. Read more about the genesis and development of napari from CZI Imaging Software Fellow and napari co-founder Juan Nuñez-Iglesias.

May 19, 2020

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