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https://github.com/xq141839/NuSegDG
[ArXiv' 24] NuSegDG: Integration of Heterogeneous Space and Gaussian Kernel for Domain-Generalized Nuclei Segmentation
https://github.com/xq141839/NuSegDG
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[ArXiv' 24] NuSegDG: Integration of Heterogeneous Space and Gaussian Kernel for Domain-Generalized Nuclei Segmentation
- Host: GitHub
- URL: https://github.com/xq141839/NuSegDG
- Owner: xq141839
- License: apache-2.0
- Created: 2024-08-21T13:22:21.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-08-29T04:37:16.000Z (5 months ago)
- Last Synced: 2024-08-29T05:45:21.590Z (5 months ago)
- Language: Python
- Size: 260 KB
- Stars: 15
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- Awesome-Segment-Anything - [code
README
# NuSegDG: Integration of Heterogeneous Space and Gaussian Kernel for Domain-Generalized Nuclei Segmentation
:pushpin: This is an official PyTorch implementation of **NuSegDG: Integration of Heterogeneous Space and Gaussian Kernel for Domain-Generalized Nuclei Segmentation**
[[`arXiv`](https://arxiv.org/abs/2408.11787)] [[`BibTeX`](https://scholar.googleusercontent.com/scholar.bib?q=info:5dd80O9YdlwJ:scholar.google.com/&output=citation&scisdr=ClEWMSDREKieyH-ljbE:AFWwaeYAAAAAZsqjlbFJ6b4dsop8Vuw6Q8w_Dzk&scisig=AFWwaeYAAAAAZsqjlUd0m9H7J9n4zZNxl9Sj-a8&scisf=4&ct=citation&cd=-1&hl=en)]
## π°News
**[2024.08.21]** The pre-print paper has been uploaded!
## π Setup
```bash
git clone https://github.com/xq141839/NuSegDG.git
cd NuSegDG
conda create -n NuSegDG python=3.10
conda activate NuSegDG
conda install pytorch==1.13.0 torchvision==0.14.0 torchaudio==0.13.0 pytorch-cuda=11.6 -c pytorch -c nvidia
pip install scikit-image -i https://pypi.tuna.tsinghua.edu.cn/simple
pip install albumentations==0.5.2 -i https://pypi.tuna.tsinghua.edu.cn/simple
pip install pytorch_lightning==1.1.0 -i https://pypi.tuna.tsinghua.edu.cn/simple
pip install monai -i https://pypi.tuna.tsinghua.edu.cn/simple
pip install timm -i https://pypi.tuna.tsinghua.edu.cn/simple
```## πData Preparation
The structure is as follows.
```
NuSegDG
βββ datasets
β βββ image_1024
β βββ TCGA-21-5784-01Z-00-DX1.png
| βββ ...
| βββ mask_1024
β βββ TCGA-21-5784-01Z-00-DX1.png
| βββ ...
| βββ DensityMap
β βββ TCGA-21-5784-01Z-00-DX1.png
| βββ ...
```## πCitation
If you find this work helpful for your project, please consider citing the following paper:
```
@article{lou2024nusegdg,
title={NuSegDG: Integration of Heterogeneous Space and Gaussian Kernel for Domain-Generalized Nuclei Segmentation},
author={Lou, Zhenye and Xu, Qing and Jiang, Zekun and He, Xiangjian and Chen, Zhen and Wang, Yi and Li, Chenxin and He, Maggie M and Duan, Wenting},
journal={arXiv preprint arXiv:2408.11787},
year={2024}
}
```## πAcknowledgements
Greatly appreciate the tremendous effort for the following projects!
- [SAM](https://github.com/facebookresearch/segment-anything)
- [Conv-LoRA](https://github.com/autogluon/autogluon/tree/master/examples/automm/Conv-LoRA)