On the pitfalls of deep image segmentation for lightsheet microscopy

Rami Al-Maskari, Johannes C. Paetzold, Izabela Horvath, Ali Erturk, bjoern menze

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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