MISSFormer: An Effective Medical Image Segmentation Transformer

Overview

MISSFormer

Code for paper "MISSFormer: An Effective Medical Image Segmentation Transformer". Please read our preprint at the following link: paper_address.

1. Environment

  • Please prepare an environment with Ubuntu 20.04, with Python 3.6.13, PyTorch 1.8.0, and CUDA 11.1.1.

2. Train/Test

  • Train
python train.py --dataset Synapse --root_path your DATA_DIR --max_epochs 400 --output_dir your OUT_DIR  --img_size 224 --base_lr 0.05 --batch_size 24
  • Test
python test.py --dataset Synapse --is_savenii --volume_path your DATA_DIR --output_dir your OUT_DIR --max_epoch 400 --base_lr 0.05 --img_size 224 --batch_size 24

References

@article{huang2021missformer,
  title={MISSFormer: An Effective Medical Image Segmentation Transformer},
  author={Huang, Xiaohong and Deng, Zhifang and Li, Dandan and Yuan, Xueguang},
  journal={arXiv preprint arXiv:2109.07162},
  year={2021}
}
Owner
Fong
Fong
Cookiecutter PyTorch Lightning

Cookiecutter PyTorch Lightning Instructions # install cookiecutter pip install cookiecutter

Mazen 8 Nov 06, 2022
This is my research project for the Irving Center for Cancer Dynamics/Azizi Lab, Columbia University.

bayesian_uncertainty This is my research project for the Irving Center for Cancer Dynamics/Azizi Lab, Columbia University. In this project I build a s

Max David Gupta 1 Feb 13, 2022
This repository contains the database and code used in the paper Embedding Arithmetic for Text-driven Image Transformation

This repository contains the database and code used in the paper Embedding Arithmetic for Text-driven Image Transformation (Guillaume Couairon, Holger

Meta Research 31 Oct 17, 2022
A booklet on machine learning systems design with exercises

Machine Learning Systems Design Read this booklet here. This booklet covers four main steps of designing a machine learning system: Project setup Data

Chip Huyen 7.6k Jan 08, 2023
Over9000 optimizer

Optimizers and tests Every result is avg of 20 runs. Dataset LR Schedule Imagenette size 128, 5 epoch Imagewoof size 128, 5 epoch Adam - baseline OneC

Mikhail Grankin 405 Nov 27, 2022
Implementation of paper: "Image Super-Resolution Using Dense Skip Connections" in PyTorch

SRDenseNet-pytorch Implementation of paper: "Image Super-Resolution Using Dense Skip Connections" in PyTorch (http://openaccess.thecvf.com/content_ICC

wxy 114 Nov 26, 2022
The official PyTorch implementation of Curriculum by Smoothing (NeurIPS 2020, Spotlight).

Curriculum by Smoothing (NeurIPS 2020) The official PyTorch implementation of Curriculum by Smoothing (NeurIPS 2020, Spotlight). For any questions reg

PAIR Lab 36 Nov 23, 2022
Pytorch implementation of the paper "Topic Modeling Revisited: A Document Graph-based Neural Network Perspective"

Graph Neural Topic Model (GNTM) This is the pytorch implementation of the paper "Topic Modeling Revisited: A Document Graph-based Neural Network Persp

Dazhong Shen 8 Sep 14, 2022
Spectralformer: Rethinking hyperspectral image classification with transformers

The code in this toolbox implements the "Spectralformer: Rethinking hyperspectral image classification with transformers". More specifically, it is detailed as follow.

Danfeng Hong 104 Jan 04, 2023
Libraries, tools and tasks created and used at DeepMind Robotics.

dm_robotics: Libraries, tools, and tasks created and used for Robotics research at DeepMind. Package overview Package Summary Transformations Rigid bo

DeepMind 273 Jan 06, 2023
A universal framework for learning timestamp-level representations of time series

TS2Vec This repository contains the official implementation for the paper Learning Timestamp-Level Representations for Time Series with Hierarchical C

Zhihan Yue 284 Dec 30, 2022
Distributed Arcface Training in Pytorch

Distributed Arcface Training in Pytorch

3 Nov 23, 2021
This is just a funny project that we want to see AutoEncoder (AE) can actually work to enhance the features we want

Funny_muscle_enhancer :) 1.Discription: This is just a funny project that we want to see AutoEncoder (AE) can actually work on the some features. We w

Jing-Yao Chen (Jacob) 8 Oct 01, 2022
Contains modeling practice materials and homework for the Computational Neuroscience course at Okinawa Institute of Science and Technology

A310 Computational Neuroscience - Okinawa Institute of Science and Technology, 2022 This repository contains modeling practice materials and homework

Sungho Hong 1 Jan 24, 2022
TigerLily: Finding drug interactions in silico with the Graph.

Drug Interaction Prediction with Tigerlily Documentation | Example Notebook | Youtube Video | Project Report Tigerlily is a TigerGraph based system de

Benedek Rozemberczki 91 Dec 30, 2022
The source code for Adaptive Kernel Graph Neural Network at AAAI2022

AKGNN The source code for Adaptive Kernel Graph Neural Network at AAAI2022. Please cite our paper if you think our work is helpful to you: @inproceedi

11 Nov 25, 2022
Fast algorithms to compute an approximation of the minimal volume oriented bounding box of a point cloud in 3D.

ApproxMVBB Status Build UnitTests Homepage Fast algorithms to compute an approximation of the minimal volume oriented bounding box of a point cloud in

Gabriel Nützi 390 Dec 31, 2022
Implementation of SiameseXML (ICML 2021)

SiameseXML Code for SiameseXML: Siamese networks meet extreme classifiers with 100M labels Best Practices for features creation Adding sub-words on to

Extreme Classification 35 Nov 06, 2022
Joint Versus Independent Multiview Hashing for Cross-View Retrieval[J] (IEEE TCYB 2021, PyTorch Code)

Thanks to the low storage cost and high query speed, cross-view hashing (CVH) has been successfully used for similarity search in multimedia retrieval. However, most existing CVH methods use all view

4 Nov 19, 2022