Journal
BIOINFORMATICS
Volume 30, Issue 17, Pages I587-I593Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu469
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Funding
- E.U [FP7 228334, FP7 284464]
- FET flagship HBP [604102]
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Motivation: Recently, confocal light sheet microscopy has enabled high-throughput acquisition of whole mouse brain 3D images at the micron scale resolution. This poses the unprecedented challenge of creating accurate digital maps of the whole set of cells in a brain. Results: We introduce a fast and scalable algorithm for fully automated cell identification. We obtained the whole digital map of Purkinje cells in mouse cerebellum consisting of a set of 3D cell center coordinates. The method is accurate and we estimated an F-1 measure of 0.96 using 56 representative volumes, totaling 1.09 GVoxel and containing 4138 manually annotated soma centers.
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