Axon Tracing and Centerline Detection using Topologically-Aware 3D U-Nets | IEEE Conference Publication | IEEE Xplore

Axon Tracing and Centerline Detection using Topologically-Aware 3D U-Nets


Abstract:

As advances in microscopy imaging provide an ever clearer window into the human brain, accurate reconstruction of neural connectivity can yield valuable insight into the ...Show More

Abstract:

As advances in microscopy imaging provide an ever clearer window into the human brain, accurate reconstruction of neural connectivity can yield valuable insight into the relationship between brain structure and function. However, human manual tracing is a slow and laborious task, and requires domain expertise. Automated methods are thus needed to enable rapid and accurate analysis at scale. In this paper, we explored deep neural networks for dense axon tracing and incorporated axon topological information into the loss function with a goal to improve the performance on both voxel-based segmentation and axon centerline detection. We evaluated three approaches using a modified 3D U-Net architecture trained on a mouse brain dataset imaged with light sheet microscopy and achieved a 10% increase in axon tracing accuracy over previous methods. Furthermore, the addition of centerline awareness in the loss function outperformed the baseline approach across all metrics, including a boost in Rand Index by 8%.
Date of Conference: 11-15 July 2022
Date Added to IEEE Xplore: 08 September 2022
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ISSN Information:

PubMed ID: 36085649
Conference Location: Glasgow, Scotland, United Kingdom

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