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Title: NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale
Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages. However, current datasets for neuronal nuclei usually contain volumes smaller than 0.01 cubic mm with fewer than 500 instances per volume, unable to reveal the complexity in large brain regions and restrict the investigation of neuronal structures. In this paper, we have pushed the task forward to the sub-cubic millimeter scale and curated the NucMM dataset with two fully annotated volumes: one 0.1 cubic mm electron microscopy (EM) volume containing nearly the entire zebra sh brain with around 170,000 nuclei; and one 0.25 cubic mm micro-CT (uCT) volume containing part of a mouse visual cortex with about 7,000 nuclei. With two imaging modalities and significantly increased volume size and instance numbers, we discover a great diversity of neuronal nuclei in appearance and density, introducing new challenges to the  eld. We also perform a statistical analysis to illustrate those challenges quantitatively. To tackle the challenges, we propose a novel hybrid-representation learning model that combines the merits of foreground mask, contour map, and signed distance transform to produce high-quality 3D masks. The benchmark comparisons on the NucMM dataset show that our proposed method significantly outperforms state-of- the-art nuclei segmentation approaches. Code and data are available at https://connectomics-bazaar.github.io/proj/nucMM/index.html.
Authors:
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Award ID(s):
1835231
Publication Date:
NSF-PAR ID:
10312226
Journal Name:
International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI)
Sponsoring Org:
National Science Foundation
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