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Imaging Bootcamp

Publicly-available dataset of rodent brain blood vessel-3D imaging for training machine learning tools to analyse biomedical images

14 April 2023

Imaging Bootcamp

Imaging blood vessels is a part of research into all sorts of conditions, from stroke to Alzheimer’s. Analysing these data requires a process called blood vessel segmentation where blood vessels are identified from non-vessel tissue. With large volumes of imaging data, segmentation needs to be automated using computer algorithms. For this to be effective, algorithms first need to be trained on existing data. This currently relies on proprietary software where training data isn’t openly available or open-source software where training data isn't comprehensively labelled with what's what. Researchers now present MiniVess, a dataset of 70 3D image volumes of rodent brain blood vessels (a selection is pictured), imaged using two-photon fluorescence microscopy and labelled in detail. This was created using U-Net, a type of deep learning called a convolutional neural network. It is publicly available and will help train algorithms to analyse future blood vessel imaging data in brain research.

Written by Lux Fatimathas

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BPoD stands for Biomedical Picture of the Day. Managed by the MRC Laboratory of Medical Sciences until Jul 2023, it is now run independently by a dedicated team of scientists and writers. The website aims to engage everyone, young and old, in the wonders of biology, and its influence on medicine. The ever-growing archive of more than 4000 research images documents over a decade of progress. Explore the collection and see what you discover. Images are kindly provided for inclusion on this website through the generosity of scientists across the globe.

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