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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:
DOI:
10.21227/48b7-s821
Data Format:
Average: 5 (1 vote)

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