Nuclei Detection for 3D Microscopy With a Fully Convolutional Regression Network.
IEEE Access
; 9: 60396-60408, 2021.
Article
em En
| MEDLINE
| ID: mdl-35024261
ABSTRACT
Advances in three-dimensional microscopy and tissue clearing are enabling whole-organ imaging with single-cell resolution. Fast and reliable image processing tools are needed to analyze the resulting image volumes, including automated cell detection, cell counting and cell analytics. Deep learning approaches have shown promising results in two- and three-dimensional nuclei detection tasks, however detecting overlapping or non-spherical nuclei of different sizes and shapes in the presence of a blurring point spread function remains challenging and often leads to incorrect nuclei merging and splitting. Here we present a new regression-based fully convolutional network that located a thousand nuclei centroids with high accuracy in under a minute when combined with V-net, a popular three-dimensional semantic-segmentation architecture. High nuclei detection F1-scores of 95.3% and 92.5% were obtained in two different whole quail embryonic hearts, a tissue type difficult to segment because of its high cell density, and heterogeneous and elliptical nuclei. Similar high scores were obtained in the mouse brain stem, demonstrating that this approach is highly transferable to nuclei of different shapes and intensities. Finally, spatial statistics were performed on the resulting centroids. The spatial distribution of nuclei obtained by our approach most resembles the spatial distribution of manually identified nuclei, indicating that this approach could serve in future spatial analyses of cell organization.
Texto completo:
1
Bases de dados:
MEDLINE
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Idioma:
En
Revista:
IEEE Access
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Estados Unidos