Lesion Segmentation

HAM10000 is a dataset of 10000 training images for detecting pigmented skin lesions. The authors collected dermatoscopic images from different populations, acquired and stored by different modalities. Source: https://www.kaggle.com/kmader/skin-cancer-mnist-ham10000 Image Source: https://www.kaggle.com/kmader/skin-cancer-mnist-ham10000

Lesion segmentation data includes the original image, paired with the expert manual tracing of the lesion boundaries in the form of a binary mask. The Training Data file is a ZIP file, containing 900 dermoscopic lesion images in JPEG format. All images are named using the scheme ISIC_<image_id>.jpg, where <image_id> is a 7-digit unique identifier. EXIF tags in the images have been removed; any remaining EXIF tags should not be relied upon to provide accurate metadata. The Training Ground Truth file is a ZIP file, containing 900 binary mask images in PNG format. All masks are named using the scheme ISIC_<image_id>_Segmentation.png, where <image_id> matches the corresponding Training Data image for the mask. All mask images will have the exact same dimensions as their corresponding lesion image. Mask images are encoded as single-channel (grayscale) 8-bit PNGs (to provide lossless compression), where each pixel is either: 0: representing the background of the image or areas outside the lesion 255: representing the foreground of the image or areas inside the lesion

The ISIC 2018 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. This Task 1 dataset is the challenge on lesion segmentation. It includes 2594 images. Source: Bi-Directional ConvLSTM U-Net with Densley Connected Convolutions Image Source: https://challenge2018.isic-archive.com/task1/

Head and Neck Tumor Segmentation

Introduced by Da et al. in DigestPath: a Benchmark Dataset with Challenge Review for the Pathological Detection and Segmentation of Digestive-System ### Grand-Challenge Page ### 1. Signet ring cell dataset Signet ring cell carcinoma is a type of rare adenocarcinoma with poor prognosis. Early detection of such cells leads to huge improvement of patients' survival rate. However, there is no existing public dataset with annotations for studying the problem of signet ring cell detection. This dataset has positive samples and negative samples. Training positive samples contain 77 images from 20 WSIs, with cell bounding boxes written in xml. Training negative samples contain 378 images from 79 WSIs.These negative WSIs have no signet ring, but could contain other kinds of tumor cells. Each signet ring cell is labeled by experienced pathologists with a rectangle bounding box tightly surrounding the cell. Each image is of size 2000X2000. The training images are from 2 organs, including gastric mucosa and intestine. Because of the difficulty of manual annotation, there exist some signet ring cells who are missed by pathologists. In other words, this dataset is a noisy dataset with its positive images not fully annotated. All whole slide images were stained by hematoxylin and eosin and scanned at X40. ### 2. Colonoscopy tissue segment dataset Colonoscopy pathology examination can find cells of early-stage colon tumor from small tissue slices. Pathologists need to daily examine hundreds of tissue slices, which is a time consuming and exhausting work. Here we propose a challenge task on automatic colonoscopy tissue segmentation and screening, aiming at automatic lesion segmentation and classification of the whole tissue (benign vs. malignant). This dataset has positive samples and negative samples. Training positive samples contain 250 images of tissue from 93 WSIs, with pixel-level annotation in jpg format, where 0 means background and 255 for foreground (malignant lesion). You could simply get binary mask by a threshold 128. Training negative samples contain 410 images of tissue from 231 WSI. This negative images have no annotation because they don't have any malignant lesion. The average size of all images are of 5000x5000 pixels, some of them are extremely huge. We will also provide another 152 patients' 212 tissues as the testing set, in which 90 images from 65 patients contain lesion. All whole slide images were stained by hematoxylin and eosin and scanned at X20. Sign the DATABASE USE AGREEMENT first and download the dataset at the homepage! Da Q, Huang X, Li Z, et al. DigestPath: a Benchmark Dataset with Challenge Review for the Pathological Detection and Segmentation of Digestive-System[J]. Medical Image Analysis, 2022: 102485. （https://doi.org/10.1016/j.media.2022.102485）

This dataset has 1,842 images with pixel-level DR-related lesion annotations, and 1,000 images with image-level labels graded by six board-certified ophthalmologists with intra-rater consistency. The proposed dataset will enable extensive studies on DR diagnosis. Source: A Benchmark for Studying Diabetic Retinopathy: Segmentation, Grading, and Transferability

CoIR (Code Information Retrieval) benchmark, is designed to evaluate code retrieval capabilities. CoIR includes 10 curated code datasets, covering 8 retrieval tasks across 7 domains. In total, it encompasses two million documents. It also provides a common and easy Python framework, installable via pip, and shares the same data schema as benchmarks like MTEB and BEIR for easy cross-benchmark evaluations.

The ISIC 2017 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. The Task 1 challenge dataset for lesion segmentation contains 2,000 images for training with ground truth segmentations (2000 binary mask images). Source: https://challenge.isic-archive.com/landing/2017/42 Image Source: https://challenge.isic-archive.com/landing/2017/42

The ISIC 2018 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. The Task 3 dataset is the challenge on lesion classification. It includes 2594 images. The task is to classify the dermoscopic images into one of the following categories: melanoma, melanocytic nevus, basal cell carcinoma, actinic keratosis / Bowen’s disease, benign keratosis, dermatofibroma, and vascular lesion. Source: Bi-Directional ConvLSTM U-Net with Densley Connected Convolutions Image Source: https://challenge2018.isic-archive.com/task3/

The SD-198 dataset contains 198 different diseases from different types of eczema, acne and various cancerous conditions. There are 6,584 images in total. A subset include the classes with more than 20 image samples, namely SD-128."

The increasing incidence of melanoma has recently promoted the development of computer-aided diagnosis systems for the classification of dermoscopic images. The PH² dataset has been developed for research and benchmarking purposes, in order to facilitate comparative studies on both segmentation and classification algorithms of dermoscopic images. PH² is a dermoscopic image database acquired at the Dermatology Service of Hospital Pedro Hispano, Matosinhos, Portugal.

Over 1.5K images selected from the public Kaggle DR Detection dataset; Five DR grades (DR0 / DR1 / DR2 / DR3 / DR4), re-labeled by a panel of 45 experienced ophthalmologists; Eight retinal lesion classes, including microaneurysm, intraretinal hemorrhage, hard exudate, cotton-wool spot, vitreous hemorrhage, preretinal hemorrhage, neovascularization and fibrous proliferation; Over 34K expert-labeled pixel-level lesion segments; Multi-task, i.e., lesion segmentation, lesion classification, and DR grading.

The dataset is maintained by VISION AND IMAGE PROCESSING LAB, University of Waterloo. The images of the dataset were extracted from the public databases DermIS and DermQuest, along with manual segmentations of the lesions. The dataset was used in the following journal publication. [1] Glaister, J., A. Wong, and D. A. Clausi, "Automatic segmentation of skin lesions from dermatological photographs using a joint probabilistic texture distinctiveness approach", IEEE Transactions on Biomedical Engineering [2] Amelard, R., J. Glaister, A. Wong, and D. A. Clausi, "High-level intuitive features (HLIFs) for intuitive skin lesion descriptionpdf", IEEE Transactions on Biomedical Engineering, vol. 62, issue 3, pp. 820-831, October, 2015. [3] Glaister, J., R. Amelard, A. Wong, and D. A. Clausi, "MSIM: Multi-Stage Illumination Modeling of Dermatological Photographs for Illumination-Corrected Skin Lesion Analysis", IEEE Transactions on Biomedical Engineering, vol. 60, issue 7, pp. 1873 - 1883, November, 2013.

The ISIC 2018 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. The Task 2 dataset is the challenge on lesion attribute detection. It includes 2594 images. The task is to detect the following dermoscopic attributes: pigment network, negative network, streaks, mila-like cysts and globules (including dots). Source: Bi-Directional ConvLSTM U-Net with Densley Connected Convolutions Image Source: https://challenge2018.isic-archive.com/task2/

The ISIC 2017 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. The Task 3 challenge dataset for lesion classification contains 2,000 images for training including 374 melanoma, 254 seborrheic keratosis and the remainder as benign nevi (1372). Source: https://challenge.isic-archive.com/landing/2017/42 Image Source: https://challenge.isic-archive.com/landing/2017/44

A whole-body FDG-PET/CT dataset with manually annotated tumor lesions (FDG-PET-CT-Lesions) 1,014 studies (900 patients)

The ISIC 2017 dataset was published by the International Skin Imaging Collaboration (ISIC) as a large-scale dataset of dermoscopy images. The Task 2 challenge dataset for lesion dermoscopic feature extraction contains the original lesion image, a corresponding superpixel mask, and superpixel-mapped expert annotations of the presence and absence of the following features: (a) network, (b) negative network, (c) streaks and (d) milia-like cysts. Source: https://challenge.isic-archive.com/landing/2017/43 Image Source: https://challenge.isic-archive.com/landing/2017/43