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bbbc-datasets

BBBC segmentation datasets as PyTorch datasets

Fluorescence microscopy images of cell nuclei from the Broad Bioimage Benchmark Collection, and a colour-coded segmentation of one of them

A Python package that downloads the segmentation datasets of the Broad Bioimage Benchmark Collection (BBBC) and loads them as PyTorch datasets, in 2D and 3D.

The Broad Bioimage Benchmark Collection is a widely used set of annotated microscopy images. bbbc-datasets downloads and manages its segmentation datasets and loads them as PyTorch Dataset objects, handling 2D and 3D images alike.

It covers 18 datasets, among them nuclei in fluorescence microscopy (the Kaggle 2018 Data Science Bowl, U2OS cells in a chemical screen), DIC images of mouse embryos, C. elegans live/dead assays, and synthetic and 3D cell images. The available datasets can be listed and filtered to 2D or 3D before downloading anything.

Install it with pip install bbbc-datasets.

The preview shows example images from BBBC038 and BBBC039, released by the Broad Institute under CC0.

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