On the pitfalls of deep image segmentation for lightsheet microscopyDownload PDF

Published: 09 May 2022, Last Modified: 12 May 2023MIDL 2022 Short PapersReaders: Everyone
Keywords: image segmentation, light sheet microscopy, neurons, blood vessels
TL;DR: This work reviews common issues with segmentation on tissue cleared light-sheet microscopy data on both human and animal samples through the example of previous publications.
Abstract: Fluorescence light sheet microscopy (LSM) of tissue cleared samples enables holistic 3D imaging of the human brain and the full murine body. While this novel imaging method creates high resolution scans and has led to an abundance of high-profile publications in the last 5 years, analysing them is not trivial and comes with complex obstacles. In this paper we present a review and discussion of our groups previous works to present best practices on both animal and human scans and guidelines to overcome these obstacles
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Paper Type: recently published or submitted journal contributions
Primary Subject Area: Segmentation
Secondary Subject Area: Application: Other
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