b3get

A python module to download Broad Bioimage Benchmark Collection images.

Usage

As a python module

import b3get

images, labels = b3get.to_numpy(6)

The call illustrated above creates 2 python lists. Each list contains a set of numpy.ndarray objects which yield the images of the dataset (images) or the labels (labels).

If you like the idea for this repo, please drop me a star. Due to time constraints, I will concentrate on dataset 06, 24 and 27. If your dataset is not among those, please consider contributing.

From the Command-line

• to list available datasets

$ b3get list
BBBC006 Human U2OS cells (out of focus) 
BBBC008 Human HT29 colon-cancer cells   
BBBC024 3D HL60 Cell Line (synthetic data)
BBBC027 3D Colon Tissue (synthetic data)

• to show the URLS for a given dataset

$ b3get show 08
https://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_images.zip
https://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_foreground.zip