# YOLO2U-Net: Detection-Guided 3D Instance Segmentation for Microscopy

arXiv: https://arxiv.org/abs/2207.06215 · HTML: https://mlsanity.com/paper/2207.06215/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 28 references that are in the map.
- First posted on arXiv 13 Jul 2022.

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

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [Rethinking Atrous Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1706.05587/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [YOLO9000: Better, Faster, Stronger](https://mlsanity.com/paper/1612.08242/) (2016)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Deep Watershed Transform for Instance Segmentation](https://mlsanity.com/paper/1611.08303/) (2016)
- [Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy](https://mlsanity.com/paper/1908.03636/) (2019)
- [3D Deeply Supervised Network for Automatic Liver Segmentation from CT Volumes](https://mlsanity.com/paper/1607.00582/) (2016)
- [Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation](https://mlsanity.com/paper/1609.01006/) (2016)
- [Mask-RCNN and U-net Ensembled for Nuclei Segmentation](https://mlsanity.com/paper/1901.10170/) (2019)
- [BshapeNet: Object Detection and Instance Segmentation with Bounding Shape Masks](https://mlsanity.com/paper/1810.10327/) (2018)

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

- [Toward a Foundation Plug-and-Play Prior for Computed Tomography Reconstruction via a Multimodal Diffusion Model](https://mlsanity.com/paper/2608.23190/) (2026)

## Abstract (arXiv)

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. In this work, we introduce a comprehensive method for accurate 3D instance segmentation of cells in the brain tissue. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with some current deep learning-based 3D instance segmentation methods.