Whole-brain microscopy image analysis

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Abstract

Recent technical developments allow for the entire mouse brain to be imaged at cellular resolution. We developed the cellfinder software to process the resulting volumes of data in such a way that these imaging methods can be fully exploited by neuroscientists. Cellfinder uses a combination of traditional computer vision and deep learning to quickly detect labelled cells throughout the brain, and then assigns them to a brain region for visualisation and analysis. Harnessing the power of deep learning for object (rather than voxel) classification speeds up analysis by orders of magnitude and simplifies training data generation. Cellfinder is fully open-source, written in Python, and is part of the BrainGlobe suite of computational neuroanatomy tools.

About the speaker

Adam is a neuroscientist and software developer at the Sainsbury Wellcome Centre, UCL. Following a PhD in neuroscience at King’s College London, and a brief stint at the Institute of Cancer Research, he moved to UCL to develop open-source neuroscience data analysis tools. Adam co-developed the cellfinder package for the analysis of whole-brain microscopy data, and co-founded the BrainGlobe initiative to develop tools and open standards for computational neuroanatomy.

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