# RCNN-SliceNet: A Slice and Cluster Approach for Nuclei Centroid Detection in Three-Dimensional Fluorescence Microscopy Images

arXiv: https://arxiv.org/abs/2106.15753 · HTML: https://mlsanity.com/paper/2106.15753/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 50 references that are in the map.
- First posted on arXiv 29 Jun 2021.

## Builds on (most cited first, 15 of 15)

- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [You Only Look Once: Unified, Real-Time Object Detection](https://mlsanity.com/paper/1506.02640/) (2015)
- [SSD: Single Shot MultiBox Detector](https://mlsanity.com/paper/1512.02325/) (2015)
- [Fast R-CNN](https://mlsanity.com/paper/1504.08083/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Rich feature hierarchies for accurate object detection and semantic segmentation](https://mlsanity.com/paper/1311.2524/) (2013)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Spatial Pyramid Pooling in Deep Convolutional Networks for Visual Recognition](https://mlsanity.com/paper/1406.4729/) (2014)
- [Deep Hough Voting for 3D Object Detection in Point Clouds](https://mlsanity.com/paper/1904.09664/) (2019)
- [Frustum PointNets for 3D Object Detection from RGB-D Data](https://mlsanity.com/paper/1711.08488/) (2017)
- [Training Deep Networks with Synthetic Data: Bridging the Reality Gap by Domain Randomization](https://mlsanity.com/paper/1804.06516/) (2018)
- [Three Dimensional Fluorescence Microscopy Image Synthesis and Segmentation](https://mlsanity.com/paper/1801.07198/) (2018)
- [Applying Faster R-CNN for Object Detection on Malaria Images](https://mlsanity.com/paper/1804.09548/) (2018)
- [ImageJ2: ImageJ for the next generation of scientific image data](https://mlsanity.com/paper/1701.05940/) (2017)

## Built on by (most cited first, 1 of 1)

- [Affine-Consistent Transformer for Multi-Class Cell Nuclei Detection](https://mlsanity.com/paper/2310.14154/) (2023)

## Abstract (arXiv)

Robust and accurate nuclei centroid detection is important for the understanding of biological structures in fluorescence microscopy images. Existing automated nuclei localization methods face three main challenges: (1) Most of object detection methods work only on 2D images and are difficult to extend to 3D volumes; (2) Segmentation-based models can be used on 3D volumes but it is computational expensive for large microscopy volumes and they have difficulty distinguishing different instances of objects; (3) Hand annotated ground truth is limited for 3D microscopy volumes. To address these issues, we present a scalable approach for nuclei centroid detection of 3D microscopy volumes. We describe the RCNN-SliceNet to detect 2D nuclei centroids for each slice of the volume from different directions and 3D agglomerative hierarchical clustering (AHC) is used to estimate the 3D centroids of nuclei in a volume. The model was trained with the synthetic microscopy data generated using Spatially Constrained Cycle-Consistent Adversarial Networks (SpCycleGAN) and tested on different types of real 3D microscopy data. Extensive experimental results demonstrate that our proposed method can accurately count and detect the nuclei centroids in a 3D microscopy volume.