NucExM Dataset for Nuclei Segmentation in Expansion Microscopy

Citation Author(s):
Leander
Lauenburg
Zudi
Lin
Ruihan
Zhang
Marcia
dos Santos
Siyu
Huang
Ignacio
Arganda-Carreras
Edward
Boyden
Hanspeter
Pfister
Donglai
Wei
Submitted by:
Zudi Lin
Last updated:
Sat, 08/06/2022 - 01:13
DOI:
10.21227/48b7-s821
Data Format:
License:
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Abstract 

 

We curated the saturated nuclei segmentation annotation for two expansion microscopy (ExM) volumes by two neuroscience experts from a day 7 post-fertilization (dpf) zebrafish brain, imaged with confocal microscopy. These volumes have an anisotropic resolution of 0.325×0.325×2.5 μm in (x, y, z) order, with an approximate tissue expansion factor of 7.0. Thus the effective resolution becomes 0.046 × 0.046 × 0.357 μm. The two volumes are of size 2048×2048×255 voxels with 9.6K and 8.8K nuclei, respectively. This dataset is named the NucExM dataset, which serves as a testbed for 3D microscopy instance segmentation systems.

Instructions: 

The dataset contains four volumes: two ExM image volumes and two 3D instance segmentation volumes. 

Funding Agency: 
National Science Foundation
Grant Number: 
1835231; 2124179