Sphere estimation network: Three-dimensional nuclei detection of fluorescence microscopy images

David Joon Ho, Daniel Mas Montserrat, Chichen Fu, Paul Salama, Kenneth W. Dunn, Edward J. Delp

Research output: Contribution to journalArticle


Purpose: Fluorescence microscopy visualizes three-dimensional subcellular structures in tissue with two-photon microscopy achieving deeper penetration into tissue. Nuclei detection, which is essential for analyzing tissue for clinical and research purposes, remains a challenging problem due to the spatial variability of nuclei. Recent advancements in deep learning techniques have enabled the analysis of fluorescence microscopy data to localize and segment nuclei. However, these localization or segmentation techniques would require additional steps to extract characteristics of nuclei. We develop a 3D convolutional neural network, called Sphere Estimation Network (SphEsNet), to extract characteristics of nuclei without any postprocessing steps. Approach: To simultaneously estimate the center locations of nuclei and their sizes, SphEsNet is composed of two branches to localize nuclei center coordinates and to estimate their radii. Synthetic microscopy volumes automatically generated using a spatially constrained cycle-consistent adversarial network are used for training the network because manually generating 3D real ground truth volumes would be extremely tedious. Results: Three SphEsNet models based on the size of nuclei were trained and tested on five real fluorescence microscopy data sets from rat kidney and mouse intestine. Our method can successfully detect nuclei in multiple locations with various sizes. In addition, our method was compared with other techniques and outperformed them based on object-level precision, recall, and F1 score. Our model achieved 89.90% for F1 score. Conclusions: SphEsNet can simultaneously localize nuclei and estimate their size without additional steps. SphEsNet can be potentially used to extract more information from nuclei in fluorescence microscopy images.

Original languageEnglish (US)
Article number044003
JournalJournal of Medical Imaging
Issue number4
StatePublished - Jul 1 2020


  • convolutional neural network
  • fluorescence microscopy
  • nuclei detection
  • synthetic volumes

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging

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