MISSFormer: An Effective Medical Image Segmentation Transformer

Related tags

Deep Learning MISSFormer
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}
}
You might also like...
[CVPR'21] FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space
[CVPR'21] FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space

FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space by Quande Liu, Cheng Chen, Ji

Quande Liu 178 Jan 6, 2023
A collection of loss functions for medical image segmentation
A collection of loss functions for medical image segmentation

A collection of loss functions for medical image segmentation

Jun 3.1k Jan 3, 2023
Medical Image Segmentation using Squeeze-and-Expansion Transformers

Medical Image Segmentation using Squeeze-and-Expansion Transformers Introduction This repository contains the code of the IJCAI'2021 paper 'Medical Im

askerlee 172 Dec 20, 2022
Segmentation for medical image.

EfficientSegmentation Introduction EfficientSegmentation is an open source, PyTorch-based segmentation framework for 3D medical image. Features A whol

null 68 Nov 28, 2022
A PyTorch implementation for V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation
A PyTorch implementation for V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation

A PyTorch implementation of V-Net Vnet is a PyTorch implementation of the paper V-Net: Fully Convolutional Neural Networks for Volumetric Medical Imag

Matthew Macy 606 Dec 21, 2022
Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.

Semi-supervised-learning-for-medical-image-segmentation. Recently, semi-supervised image segmentation has become a hot topic in medical image computin

Healthcare Intelligence Laboratory 1.3k Jan 3, 2023
A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation

A 3D multi-modal medical image segmentation library in PyTorch We strongly believe in open and reproducible deep learning research. Our goal is to imp

Adaloglou Nikolas 1.2k Dec 27, 2022
Bayesian Optimization Library for Medical Image Segmentation.

bayesmedaug: Bayesian Optimization Library for Medical Image Segmentation. bayesmedaug optimizes your data augmentation hyperparameters for medical im

Şafak Bilici 7 Feb 10, 2022
A keras-based real-time model for medical image segmentation (CFPNet-M)
A keras-based real-time model for medical image segmentation (CFPNet-M)

CFPNet-M: A Light-Weight Encoder-Decoder Based Network for Multimodal Biomedical Image Real-Time Segmentation This repository contains the implementat

null 268 Nov 27, 2022
Comments
  • Different sizes for train and test

    Different sizes for train and test

    HI It appears that image size for training is 224 but in the test time model has been evaluated with 512 inputs. why input size for train and test are different?

    opened by saleknia 0
  • About data augmentation

    About data augmentation

    First, I am very honored to read your paper and also impressed by your excellent experiment result on synapse dataset, and I noticed that you used a lot of extra data augment methods in your dataset_synapse.py, like Gaussiannoise, while TransUnet didn't. And I am wondering how much performance these data augment methods help your model get?And how did your model perform without these methods? Thank you for your reply.

    opened by zerone-fg 0
Owner
Fong
Fong
GitHub
CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation

CoTr: Efficient 3D Medical Image Segmentation by bridging CNN and Transformer This is the official pytorch implementation of the CoTr: Paper: CoTr: Ef

null 218 Dec 25, 2022
The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"

Swin-Unet The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"(https://arxiv.org/abs/2105.05537). A validatio

null 869 Jan 7, 2023
Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation

Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation. Generally, MAS methods register multiple atlases, i.e., medical images with corresponding labels, to a target image;

NanYoMy 13 Oct 9, 2022
Copy Paste positive polyp using poisson image blending for medical image segmentation

Copy Paste positive polyp using poisson image blending for medical image segmentation According poisson image blending I've completely used it for bio

Phạm Vũ Hùng 2 Oct 19, 2021
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

MIC-DKFZ 1.2k Jan 4, 2023
Build a medical knowledge graph based on Unified Language Medical System (UMLS)

UMLS-Graph Build a medical knowledge graph based on Unified Language Medical System (UMLS) Requisite Install MySQL Server 5.6 and import UMLS data int

Donghua Chen 6 Dec 25, 2022
nnFormer: Interleaved Transformer for Volumetric Segmentation Code for paper "nnFormer: Interleaved Transformer for Volumetric Segmentation "

nnFormer: Interleaved Transformer for Volumetric Segmentation Code for paper "nnFormer: Interleaved Transformer for Volumetric Segmentation ". Please

jsguo 610 Dec 28, 2022
Vision Transformer for 3D medical image registration (Pytorch).

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

Junyu Chen 192 Dec 20, 2022
ViDT: An Efficient and Effective Fully Transformer-based Object Detector

ViDT: An Efficient and Effective Fully Transformer-based Object Detector by Hwanjun Song1, Deqing Sun2, Sanghyuk Chun1, Varun Jampani2, Dongyoon Han1,

NAVER AI 262 Dec 27, 2022
This repo holds code for TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation

TransUNet This repo holds code for TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation Usage

null 1.4k Jan 4, 2023