Dataset

Here's a brief introduction of the dataset and disease that our MedSAM Adapter support now.

2D

ISIC2016

This is a 2D dataset of melanoma or nevus segmentation from dermoscopic images and contains one foreground category. Availabel here: ISIC Challenge (isic-archive.com)

REFUGE2

This is a 2D dataset of optic disc and optic cup segmentation over fundus images and contains two foreground category. Available here: Program - Grand Challenge (grand-challenge.org)

LIDC

This is a 2D dataset of lung images and contains one foreground category. Available here: LIDC-IDRI Dataset | Papers With Code

DDTI

This is a 2D dataset for thyroid nodule segmentation and contains one foreground category . Available here: DDTI: Thyroid Ultrasound Images (kaggle.com)****

WBC

This is a 2D dataset of **white blood cell **and contains two foreground category. Available here: zxaoyou/segmentation_WBC: White blood cell (WBC) image datasets (github.com)

This dataset contains 2 sub datasets, here we use Dataset1. You can change it in dataset/wbc.py.

STARE

This is a 2D dataset of **retinal blood vessel **and contains one foreground category. Available here: https://paperswithcode.com/dataset/stare

Can be appointed by python train.py -dataset STARE ...

Pendal

This is a 2D dataset of mandible and contains one foreground category. Available here: https://data.mendeley.com/datasets/hxt48yk462/2.

Can be appointed by python train.py -dataset pendal ...

This dataset contains 2 kind of segmentation labels, in folder Segmentation1 and Segmentation2. Here we use the labels in Segmentation1 as default. This can be changed in dataset/pendal.py.

3D

Brat2021

This is a 3D dataset of brain tumors that come from the MICCAI23 challenge and contains three foreground category. Available here: MICCAI BRATS - The Multimodal Brain Tumor Segmentation Challenge

Kits23

This is a 3D dataset of kidney tumors that come from the MICCAI23 challenge and contains two foreground category. Available here: https://kits-challenge.org/kits21/. This dataset contains 2 kind of segmentation labels, namely aggregated_AND_seg.nii.gz， aggregated_OR_seg.nii.gz， aggregated_MAJ_seg.nii.gz. You can change it in dataset/kits.py.

Can be appointed by python train.py -dataset kits ...

Atlas 23

This is a 3D dataset of liver tumors that come from the MICCAI23 challenge and contains two foreground category. Available here: https://atlas-challenge.u-bourgogne.fr/dataset.

Can be appointed by python train.py -dataset atlas ...

LNQ 23

This is a 3D dataset of mediastinal lymph node that come from the MICCAI23 challenge and contains one foreground category. Available here: https://lnq2023.grand-challenge.org/ .

Can be appointed by python train.py -dataset lnq ...

SegRap

This is a 3D dataset of nasopharynx cancer from the MICCAI23 challenge and contains 53 foreground category. Available here: https://segrap2023.grand-challenge.org/segrap2023/

We use synthesized imagesimage.nii.gz for each case in folderSegRap2023_Training_Set_120cases. As for the labels, we use the labels in SegRap2023_Training_Set_120cases_OneHot_Labels\Task001, you can try different kind of labels in the original dataset as well !

Can be appointed by python train.py -dataset segrap ...

Toothfairy

This is a 3D dataset of inferior alveolar nerve from the MICCAI23 challenge and contains one foreground category. Available here: https://toothfairy.grand-challenge.org/

Can be appointed by python train.py -dataset toothfairy ...