The Raider dataset collects fMRI recordings of 1000 voxels from the ventral temporal cortex, for 10 healthy adult participants passively watching the full-length movie “Raiders of the Lost Ark”.
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The m2cai16-tool-locations dataset contains spatial tool annotations for 2,532 frames across the first 10 videos in the m2cai16-tool dataset, which includes 15 videos in total. The dataset consists of 3,141 annotations of 7 surgical instrument classes, with an average of 1.2 labels per frame and 7 instrument classes per video.
This brain anatomy segmentation dataset has 1300 2D US scans for training and 329 for testing. A total of 1629 in vivo B-mode US images were obtained from 20 different subjects (age<1 years old) who were treated between 2010 and 2016. The dataset contained subjects with IVH and without (healthy subjects but in risk of developing IVH). The US scans were collected using a Philips US machine with a C8-5 broadband curved array transducer using coronal and sagittal scan planes. For every collected image ventricles and septum pellecudi are manually segmented by an expert ultrasonographer. We split these images randomly into 1300 Training images and 329 Testing images for experiments. Note that these images are of size 512 × 512.
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The CHB-MIT dataset is a dataset of EEG recordings from pediatric subjects with intractable seizures. Subjects were monitored for up to several days following withdrawal of anti-seizure mediation in order to characterize their seizures and assess their candidacy for surgical intervention. The dataset contains 23 patients divided among 24 cases (a patient has 2 recordings, 1.5 years apart). The dataset consists of 969 Hours of scalp EEG recordings with 173 seizures. There exist various types of seizures in the dataset (clonic, atonic, tonic). The diversity of patients (Male, Female, 10-22 years old) and different types of seizures contained in the datasets are ideal for assessing the performance of automatic seizure detection methods in realistic settings.
CODA-19 is a human-annotated dataset that denotes the Background, Purpose, Method, Finding/Contribution, and Other for 10,966 English abstracts in the COVID-19 Open Research Dataset.
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The CheXmask Database presents a comprehensive, uniformly annotated collection of chest radiographs, constructed from five public databases: ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest and VinDr-CXR. The database aggregates 657,566 anatomical segmentation masks derived from images which have been processed using the HybridGNet model to ensure consistent, high-quality segmentation. To confirm the quality of the segmentations, we include in this database individual Reverse Classification Accuracy (RCA) scores for each of the segmentation masks. This dataset is intended to catalyze further innovation and refinement in the field of semantic chest X-ray analysis, offering a significant resource for researchers in the medical imaging domain.
DRTiD is a benchmark dataset for DR grading, consisting of 3,100 two-field fundus images.
DiagSet is a histopathological dataset for prostate cancer detection. The proposed dataset consists of over 2.6 million tissue patches extracted from 430 fully annotated scans, 4675 scans with assigned binary diagnosis, and 46 scans with diagnosis given independently by a group of histopathologists.
ESAD is a large-scale dataset designed to tackle the problem of surgeon action detection in endoscopic minimally invasive surgery. ESAD aims at contributing to increase the effectiveness and reliability of surgical assistant robots by realistically testing their awareness of the actions performed by a surgeon. The dataset provides bounding box annotation for 21 action classes on real endoscopic video frames captured during prostatectomy, and was used as the basis of a recent MIDL 2020 challenge.
Fundus Image Registration Dataset (FIRE) is a dataset consisting of 129 retinal images forming 134 image pairs. These image pairs are split into 3 different categories depending on their characteristics. The images were acquired with a Nidek AFC-210 fundus camera, which acquires images with a resolution of 2912x2912 pixels and a FOV of 45° both in the x and y dimensions. Images were acquired at the Papageorgiou Hospital, Aristotle University of Thessaloniki, Thessaloniki from 39 patients.
GLOBEM is a multi-year passive sensing datasets, containing over 700 user-years and 497 unique users' data collected from mobile and wearable sensors, together with a wide range of well-being metrics. The datasets can support multiple cross-dataset evaluations of behavior modeling algorithms' generalizability across different users and years.
Digital radiography is widely available and the standard modality in trauma imaging, often enabling to diagnose pediatric wrist fractures. However, image interpretation requires time-consuming specialized training. Due to astonishing progress in computer vision algorithms, automated fracture detection has become a topic of research interest. This paper presents the GRAZPEDWRI-DX dataset containing annotated pediatric trauma wrist radiographs of 6,091 patients, treated at the Department for Pediatric Surgery of the University Hospital Graz between 2008 and 2018. A total number of 10,643 studies (20,327 images) are made available, typically covering posteroanterior and lateral projections. The dataset is annotated with 74,459 image tags and features 67,771 labeled objects. We de-identified all radiographs and converted the DICOM pixel data to 16-Bit grayscale PNG images. The filenames and the accompanying text files provide basic patient information (age, sex). Several pediatric radiolog
The IS-A dataset is a dataset of relations extracted from a medical ontology. The different entities in the ontology are related by the “is a” relation. For example, ‘acute leukemia’ is a ‘leukemia’. The dataset has 294,693 nodes with 356,541 edges between them.
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).
The LIMUC dataset is the largest publicly available labeled ulcerative colitis dataset that compromises 11276 images from 564 patients and 1043 colonoscopy procedures. Three experienced gastroenterologists were involved in the annotation process, and all images are labeled according to the Mayo endoscopic score (MES).
The Medical Dataset for Abbreviation Disambiguation for Natural Language Understanding (MeDAL) is a large medical text dataset curated for abbreviation disambiguation, designed for natural language understanding pre-training in the medical domain. It was published at the ClinicalNLP workshop at EMNLP.
For each dataset we provide a short description as well as some characterization metrics. It includes the number of instances (m), number of attributes (d), number of labels (q), cardinality (Card), density (Dens), diversity (Div), average Imbalance Ratio per label (avgIR), ratio of unconditionally dependent label pairs by chi-square test (rDep) and complexity, defined as m × q × d as in [Read 2010]. Cardinality measures the average number of labels associated with each instance, and density is defined as cardinality divided by the number of labels. Diversity represents the percentage of labelsets present in the dataset divided by the number of possible labelsets. The avgIR measures the average degree of imbalance of all labels, the greater avgIR, the greater the imbalance of the dataset. Finally, rDep measures the proportion of pairs of labels that are dependent at 99% confidence. A broader description of all the characterization metrics and the used partition methods are described in
Clinical diagnosis of the eye is performed over multifarious data modalities including scalar clinical labels, vectorized biomarkers, two-dimensional fundus images, and three-dimensional Optical Coherence Tomography (OCT) scans. While the clinical labels, fundus images and OCT scans are instrumental measurements, the vectorized biomarkers are interpreted attributes from the other measurements. Clinical practitioners use all these data modalities for diagnosing and treating eye diseases like Diabetic Retinopathy (DR) or Diabetic Macular Edema (DME). Enabling usage of machine learning algorithms within the ophthalmic medical domain requires research into the relationships and interactions between these relevant data modalities. Existing datasets are limited in that: (i) they view the problem as disease prediction without assessing biomarkers, and (ii) they do not consider the explicit relationship among all four data modalities over the treatment period. In this paper, we introduce the O
Electrocardiography (ECG) is a key diagnostic tool to assess the cardiac condition of a patient. Automatic ECG interpretation algorithms as diagnosis support systems promise large reliefs for the medical personnel - only on the basis of the number of ECGs that are routinely taken. However, the development of such algorithms requires large training datasets and clear benchmark procedures. In our opinion, both aspects are not covered satisfactorily by existing freely accessible ECG datasets.
Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of similar data in the medical field, specifically in histopathology, has halted similar progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models), handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets, from other sources, including Twitter, research papers, and the internet in general, to create an even larger dat
The RITE (Retinal Images vessel Tree Extraction) is a database that enables comparative studies on segmentation or classification of arteries and veins on retinal fundus images, which is established based on the public available DRIVE database (Digital Retinal Images for Vessel Extraction).
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Endoscopic stereo reconstruction for surgical scenes gives rise to specific problems, including the lack of clear corner features, highly specular surface properties, and the presence of blood and smoke. These issues present difficulties for both stereo reconstruction itself and also for standardised dataset production. We present a stereo-endoscopic reconstruction validation dataset based on cone-beam CT (SERV-CT). Two ex vivo small porcine full torso cadavers were placed within the view of the endoscope with both the endoscope and target anatomy visible in the CT scan. Subsequent orientation of the endoscope was manually aligned to match the stereoscopic view and benchmark disparities, depths and occlusions are calculated. The requirement of a CT scan limited the number of stereo pairs to 8 from each ex vivo sample. For the second sample an RGB surface was acquired to aid alignment of smooth, featureless surfaces. Repeated manual alignments showed an RMS disparity accuracy of around
Histopathological characterization of colorectal polyps allows to tailor patients' management and follow up with the ultimate aim of avoiding or promptly detecting an invasive carcinoma. Colorectal polyps characterization relies on the histological analysis of tissue samples to determine the polyps malignancy and dysplasia grade. Deep neural networks achieve outstanding accuracy in medical patterns recognition, however they require large sets of annotated training images. We introduce UniToPatho, an annotated dataset of 9536 hematoxylin and eosin stained patches extracted from 292 whole-slide images, meant for training deep neural networks for colorectal polyps classification and adenomas grading. The slides are acquired through a Hamamatsu Nanozoomer S210 scanner at 20× magnification (0.4415 μm/px)
The eICU Collaborative Research Database is a large multi-center critical care database made available by Philips Healthcare in partnership with the MIT Laboratory for Computational Physiology.
Autism spectrum disorder (ASD) is characterized by qualitative impairment in social reciprocity, and by repetitive, restricted, and stereotyped behaviors/interests. Previously considered rare, ASD is now recognized to occur in more than 1% of children. Despite continuing research advances, their pace and clinical impact have not kept up with the urgency to identify ways of determining the diagnosis at earlier ages, selecting optimal treatments, and predicting outcomes. For the most part this is due to the complexity and heterogeneity of ASD. To face these challenges, large-scale samples are essential, but single laboratories cannot obtain sufficiently large datasets to reveal the brain mechanisms underlying ASD. In response, the Autism Brain Imaging Data Exchange (ABIDE) initiative has aggregated functional and structural brain imaging data collected from laboratories around the world to accelerate our understanding of the neural bases of autism. With the ultimate goal of facilitating
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A dataset of 12-lead ECGs with annotations. The dataset contains 345 779 exams from 233 770 patients. It was obtained through stratified sampling from the CODE dataset ( 15% of the patients). The data was collected by the Telehealth Network of Minas Gerais in the period between 2010 and 2016.
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Three-dimensional position of external markers placed on the chest and abdomen of healthy individuals breathing during intervals from 73s to 222s. The markers move because of the respiratory motion, and their position is sampled at approximately 10Hz. Markers are metallic objects used during external beam radiotherapy to track and predict the motion of tumors due to breathing for accurate dose delivery.
The dataset contains a Video capsule endoscopy dataset for polyp segmentation.
LKS is a dataset of 684 Liver-Kidney-Stomach immunofluorescence whole slide images (WSIs) used in the investigation of autoimmune liver disease.
MIMIC-CXR-LT. We construct a single-label, long-tailed version of MIMIC-CXR in a similar manner. MIMIC-CXR is a multi-label classification dataset with over 200,000 chest X-rays labeled with 13 pathologies and a “No Findings” class. The resulting MIMIC-CXR-LT dataset contains 19 classes, of which 10 are head classes, 6 are medium classes, and 3 are tail classes. MIMIC-CXR-LT contains 111,792 images labeled with one of 18 diseases, with 87,493 training images and 23,550 test set images. The validation and balanced test sets contain 15 and 30 images per class, respectively.
MIMIC-IV-ED is a large, freely available database of emergency department (ED) admissions at the Beth Israel Deaconess Medical Center between 2011 and 2019. As of MIMIC-ED v1.0, the database contains 448,972 ED stays. Vital signs, triage information, medication reconciliation, medication administration, and discharge diagnoses are available. All data are deidentified to comply with the Health Information Portability and Accountability Act (HIPAA) Safe Harbor provision. MIMIC-ED is intended to support a diverse range of education initiatives and research studies.
This database includes 25 long-term ECG recordings of human subjects with atrial fibrillation (mostly paroxysmal).
The “Medico automatic polyp segmentation challenge” aims to develop computer-aided diagnosis systems for automatic polyp segmentation to detect all types of polyps (for example, irregular polyp, smaller or flat polyps) with high efficiency and accuracy. The main goal of the challenge is to benchmark semantic segmentation algorithms on a publicly available dataset, emphasizing robustness, speed, and generalization.
NIH-CXR-LT. NIH ChestXRay14 contains over 100,000 chest X-rays labeled with 14 pathologies, plus a “No Findings” class. We construct a single-label, long-tailed version of the NIH ChestXRay14 dataset by introducing five new disease findings described above. The resulting NIH-CXR-LT dataset has 20 classes, including 7 head classes, 10 medium classes, and 3 tail classes. NIH-CXR-LT contains 88,637 images labeled with one of 19 thorax diseases, with 68,058 training and 20,279 test images. The validation and balanced test sets contain 15 and 30 images per class, respectively.
The OCTAGON dataset is a set of Angiography by Octical Coherence Tomography images (OCT-A) used to the segmentation of the Foveal Avascular Zone (FAZ). The dataset includes 144 healthy OCT-A images and 69 diabetic OCT-A images, divided into four groups, each one with 36 and about 17 OCT-A images, respectively. These groups are: 3x3 superficial, 3x3 deep, 6x6 superficial and 6x6 deep, where 3x3 and 6x6 are the zoom of the image and superficial/deep are the depth level of the extracted image. The healthy dataset includes OCT-A images from people classified in 6 age ranges: 10-19 years, 20-29 years, 30-39 years, 40-49 years, 50-59 years and 60-69 years. Each age range includes 3 different patients with information of left and right eyes for each one. Finally, for each eye, there are four different images: one 3x3 superficial image, one 3x3 deep image, one 6x6 superficial image and one 6x6 deep image. Each image have two manual labelled of expert clinicians of the FAZ and their quantificat
The ORVS dataset has been newly established as a collaboration between the computer science and visual-science departments at the University of Calgary.
OVQA contains 19,020 medical visual question and answer pairs generated from 2,001 medical images collected from 2,212 EMRs in Orthopedics.
Overview This database of simulated arterial pulse waves is designed to be representative of a sample of pulse waves measured from healthy adults. It contains pulse waves for 4,374 virtual subjects, aged from 25-75 years old (in 10 year increments). The database contains a baseline set of pulse waves for each of the six age groups, created using cardiovascular properties (such as heart rate and arterial stiffness) which are representative of healthy subjects at each age group. It also contains 728 further virtual subjects at each age group, in which each of the cardiovascular properties are varied within normal ranges. This allows for extensive in silico analyses of haemodynamics and the performance of pulse wave analysis algorithms.
Phee is a dataset for pharmacovigilance comprising over 5000 annotated events from medical case reports and biomedical literature. It is designed for biomedical event extraction tasks.
This prostate MRI segmentation dataset is collected from six different data sources.
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Purpose Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered cone-beam CT (CBCT) and magnetic resonance imaging (MRI) images to facilitate the development and evaluation of sCT generation for radiotherapy planning.
A vast amount of information in the biomedical domain is available as natural language free text. An increasing number of documents in the field are written in languages other than English. Therefore, it is essential to develop resources, methods and tools that address Natural Language Processing in the variety of languages used by the biomedical community. In this paper, we report on the development of an extensive corpus of biomedical documents in French annotated at the entity and concept level. Three text genres are covered, comprising a total of 103,056 words. Ten entity categories corresponding to UMLS Semantic Groups were annotated, using automatic pre-annotations validated by trained human annotators. The pre-annotation method was found helful for entities and achieved above 0.83 precision for all text genres. Overall, a total of 26,409 entity annotations were mapped to 5,797 unique UMLS concepts.
Thyroid is a dataset for detection of thyroid diseases, in which patients diagnosed with hypothyroid or subnormal are anomalies against normal patients. It contains 2800 training data instance and 972 test instances, with 29 or so attributes.
The US-4 is a dataset of Ultrasound (US) images. It is a video-based image dataset that contains over 23,000 high-resolution images from four US video sub-datasets, where two sub-datasets are newly collected by experienced doctors for this dataset.
VinDr-RibCXR is a benchmark dataset for automatic segmentation and labeling of individual ribs from chest X-ray (CXR) scans. The VinDr-RibCXR contains 245 CXRs with corresponding ground truth annotations provided by human experts.
Attention Deficit Hyperactivity Disorder (ADHD) affects at least 5-10% of school-age children and is associated with substantial lifelong impairment, with annual direct costs exceeding $36 billion/year in the US. Despite a voluminous empirical literature, the scientific community remains without a comprehensive model of the pathophysiology of ADHD. Further, the clinical community remains without objective biological tools capable of informing the diagnosis of ADHD for an individual or guiding clinicians in their decision-making regarding treatment.
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