Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge. Through FetReg2021 challenge, we released the first large-scale multi-centre dataset of fetoscopy laser photocoagulation procedure. The dataset contains 2,718 pixel-wise annotated images (for background, vessel, fetus, tool classes) from 24 different in vivo TTTS fetoscopic surgeries and 24 unannotated video clips video clips containing 9,616 frames for training and testing. The dataset is useful for the development of generalized and robust semantic segmentation and video mosaicking algorithms for long duration fetoscopy videos.
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Kvasir-Capsule dataset is the largest publicly released VCE dataset. In total, the dataset contains 47,238 labeled images and 117 videos, where it captures anatomical landmarks and pathological and normal findings. The results is more than 4,741,621 images and video frames altogether.
the MTHS dataset contains 30Hz PPG signals obtained from 62 patients, including 35 men and 27 women. The ground truth data includes heart rate and oxygen saturation levels sampled at 1Hz. The HR and SPo2 measurement is obtained using a pulse oximeter (M70). An iPhone 5s was used to obtain the ppg recordings at 30 fps.
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The PAX-Ray++ dataset uses pseudo-labeled thorax CTs to enable the segmentation of anatomy in Chest X-Rays. By projecting the CTs to a 2D plane, we gather fine-grained annotated imaages resembling radiographs. It contains 7,377 frontal and lateral view images each with 157 anatomy classes and over 2 million annotated instances.
Placenta is a benchmark dataset for node classification in an underexplored domain: predicting microanatomical tissue structures from cell graphs in placenta histology whole slide images. Cell graphs are large (>1 million nodes per image), node features are varied (64-dimensions of 11 types of cells), class labels are imbalanced (9 classes ranging from 0.21% of the data to 40.0%), and cellular communities cluster into heterogeneously distributed tissues of widely varying sizes (from 11 nodes to 44,671 nodes for a single structure).
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Electrophysiological data from implanted electrodes in the human brain are rare, and therefore scientific access to it has remained somewhat exclusive. Here we present a freely-available curated library of implanted electrocorticographic (ECoG) data and analyses for 16 benchmark behavioral experiments, with 204 individual datasets from 34 patients made with the same amplifiers (at the same sampling rate and filter settings). In every case, electrode positions have been carefully registered to brain anatomy. A large set of fully-commented analysis scripts to interpret these data using modern techniques is embedded in the library alongside the data. All data, anatomic correlations, and analysis files (MATLAB code) are in a common, intuitive file structure at https://searchworks.stanford.edu/view/zk881ps0522. The library may be used as course material or serve as a starter package for researchers early in their career or for established groups, to modify the analyses and re-apply them in
This mouse cerebellar atlas can be used for mouse cerebellar morphometry.
By releasing this dataset, we aim at providing a new testbed for computer vision techniques using Deep Learning. The main peculiarity is the shift from the domain of "natural images" proper of common benchmark dataset to biological imaging. We anticipate that the advantages of doing so could be two-fold: i) fostering research in biomedical-related fields - for which popular pre-trained models perform typically poorly - and ii) promoting methodological research in deep learning by addressing peculiar requirements of these images. Possible applications include but are not limited to semantic segmentation, object detection and object counting. The data consist of 283 high-resolution pictures (1600x1200 pixels) of mice brain slices acquired through a fluorescence microscope. The final goal is to individuate and count neurons highlighted in the pictures by means of a marker, so to assess the result of a biological experiment. The corresponding ground-truth labels were generated through a hy
A curated evaluation dataset for end-to-end Relation Extraction of relationships between organisms and natural-products.
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This dataset is a collection of fluorescent images from mice in order to test an automatic cell counting tool that we developed. 62 images viewed from 2 or 3 different fields of views are shown. In brief, the dataset was derived from brain sections of a model for HIV-induced brain injury (HIVgp120tg), which expresses soluble gp120 envelope protein in astrocytes under the control of a modified GFAP promoter. The mice were in a mixed C57BL/6.129/SJL genetic background, and two genotypes of 9 month old male mice were selected: wild type controls (Resting, n = 3) and transgenic littermates (HIVgp120tg, Activated, n = 3). No randomization was performed. HIVgp120tg mice show among other hallmarks of human HIV neuropathology an increase in microglia numbers which indicates activation of the cells compared to non-transgenic littermate controls.
BioLeaflets is a biomedical dataset for Data2Text generation. It is a corpus of 1,336 package leaflets of medicines authorised in Europe, which were obtained by scraping the European Medicines Agency (EMA) website. Package leaflets are included in the packaging of medicinal products and contain information to help patients use the product safely and appropriately, under the guidance of their healthcare professional. Each document contains six sections: 1) What is the product and what is it used for 2) What you need to know before you take the product 3) product usage instructions 4) possible side effects, 5) product storage conditions 6) other information.
To advance methods for pain assessment, in particular automatic assessment methods, the BioVid Heat Pain Database was collected in a collaboration of the Neuro-Information Technology group of the University of Magdeburg and the Medical Psychology group of the University of Ulm. In our study, 90 participants were subjected to experimentally induced heat pain in four intensities. To compensate for varying heat pain sensitivities, the stimulation temperatures were adjusted based on the subject-specific pain threshold and pain tolerance. Each of the four pain levels was stimulated 20 times in randomized order. For each stimulus, the maximum temperature was held for 4 seconds. The pauses between the stimuli were randomized between 8-12 seconds. The pain stimulation experiment was conducted twice: once with un-occluded face and once with facial EMG sensors.
Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present the real results severity (BIRADS) and pathology (post-report) classifications provided by the Radiologist Director from the Radiology Department of Hospital Fernando Fonseca while diagnosing several patients (see dataset-uta4-dicom) from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset for the measurements of both severity (BIRADS) and pathology classifications concerning the patient diagnostic. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted from our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these t
Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present our medical imaging DICOM files of patients from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset of the used medical images during the UTA4 tasks. This repository and respective dataset should be paired with the dataset-uta4-rates repository dataset. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted on our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby dataset repres
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Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present our severity rates (BIRADS) of clinicians while diagnosing several patients from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset for the measurements of severity rates (BIRADS) concerning the patient diagnostic. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted from our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby dataset represents the pieces of information of bot
This is a set of 100,000 non-overlapping image patches from hematoxylin & eosin (H&E) stained histological images of human colorectal cancer (CRC) and normal tissue. All images are 224x224 pixels (px) at 0.5 microns per pixel (MPP). For tissue classification; the classes are: Adipose (ADI), background (BACK), debris (DEB), lymphocytes (LYM), mucus (MUC), smooth muscle (MUS), normal colon mucosa (NORM), cancer-associated stroma (STR), colorectal adenocarcinoma epithelium (TUM). The images were manually extracted from N=86 H&E stained human cancer tissue slides from formalin-fixed paraffin-embedded (FFPE) samples from the NCT Biobank (National Center for Tumor Diseases, Heidelberg, Germany) and the UMM pathology archive (University Medical Center Mannheim, Mannheim, Germany). Tissue samples contained CRC primary tumor slides and tumor tissue from CRC liver metastases; normal tissue classes were augmented with non-tumorous regions from gastrectomy specimen to increase variability.
CheXlocalize is a radiologist-annotated segmentation dataset on chest X-rays. The dataset consists of two types of radiologist annotations for the localization of 10 pathologies: pixel-level segmentations and most-representative points. Annotations were drawn on images from the CheXpert validation and test sets. The dataset also consists of two separate sets of radiologist annotations: (1) ground-truth pixel-level segmentations on the validation and test sets, drawn by two board-certified radiologists, and (2) benchmark pixel-level segmentations and most-representative points on the test set, drawn by a separate group of three board-certified radiologists.
This collection contains data and code associated with the IPCAI/IJCARS 2020 paper “Automatic Annotation of Hip Anatomy in Fluoroscopy for Robust and Efficient 2D/3D Registration.” The data hosted here consists of annotated datasets of actual hip fluoroscopy, CT and derived data from six lower torso cadaveric specimens. Documentation and examples for using the dataset and Python code for training and testing the proposed models are also included. Higher-level information, including clinical motivations, prior works, algorithmic details, applications to 2D/3D registration, and experimental details, may be found in the companion paper which is available at https://arxiv.org/abs/1911.07042 or https://doi.org/10.1007/s11548-020-02162-7. We hope that this code and data will be useful in the development of new computer-assisted capabilities that leverage fluoroscopy.
The data presented here was extracted from a larger dataset collected through a collaboration between the Embedded Systems Laboratory (ESL) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland and the Institute of Sports Sciences of the University of Lausanne (ISSUL). In this dataset, we report the extracted segments used for an analysis of R peak detection algorithms during high intensity exercise.
This is the supplemental data for our paper on how to benchmark registrations of serial sections with ground truths. There are three main modalities and one further, as a reference.
The dataset X of this work is an extension of the heartSeg dataset. Each sample x ∈ X is an RGB image capturing the heart region of Medaka (Oryzias latipes) hatchlings from a constant ventral view. Since the body of Medaka is see-through, noninvasive studies regarding the internal organs and the whole circulatory system are practicable. A Medaka’s heart contains three parts: the atrium, the ventricle, and the bulbus. The atrium receives deoxygenated blood from the circulatory system and delivers it to the ventricle, which forwards it into the bulbus. The bulbus is the heart’s exit chamber and provides the gill arches with a constant blood flow. The blood flow through these three chambers was captured in 63 short recordings (around 11 seconds with 24 frames per second each) in total, from which the single image samples x ∈ X are extracted. The dataset is split into training and test data following the heartSeg dataset with ntrain = 565 samples in the training set Xtrain and ntest = 165
The Fraunhofer Portugal AICOS EDoF Dataset was produced within the TAMI project and is composed of images of microscopic fields of view (FOV) of Liquid-based Cervical Cytology (LBC) samples. A total of 15 LBC samples were supplied by the Pathology Services from Hospital Fernando Fonseca and the Portuguese Oncology Institute of Porto. For each LBC sample, a set of images were obtained using a version of µSmartScope [1,2] prototype adapted to the cervical cytology use case [3,4].
The dataset contains full-spectral autofluorescence lifetime microscopic images (FS-FLIM) acquired on unstained ex-vivo human lung tissue, where 100 4D hypercubes of 256x256 (spatial resolution) x 32 (time bins) x 512 (spectral channels from 500nm to 780nm). This dataset associates with our paper "Deep Learning-Assisted Co-registration of Full-Spectral Autofluorescence Lifetime Microscopic Images with H&E-Stained Histology Images" (https://arxiv.org/abs/2202.07755) and "Full spectrum fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution" (https://doi.org/10.1038/s41467-021-26837-0). The FS-FLIM images provide transformative insights into human lung cancer with extra-dimensional information. This will enable visual and precise detection of early lung cancer. With the methodology in our co-registration paper, FS-FLIM images can be registered with H&E-stained histology images, allowing characterisation of tumour and surrounding cells at a celluar level with abs
The National Health and Nutrition Examination Survey (NHANES) provides data on the health and environmental exposure of the non-institutionalized US population. Such data have considerable potential to understand how the environment and behaviors impact human health. These data are also currently leveraged to answer public health questions such as prevalence of disease. However, these data need to first be processed before new insights can be derived through large-scale analyses. NHANES data are stored across hundreds of files with multiple inconsistencies. Correcting such inconsistencies takes systematic cross examination and considerable efforts but is required for accurately and reproducibly characterizing the associations between the exposome and diseases (e.g., cancer mortality outcomes). Thus, we developed a set of curated and unified datasets and accompanied code by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-20
The image set contains 180 high-resolution color microscopic images of human duodenum adenocarcinoma HuTu 80 cell populations obtained in an in vitro scratch assay (for the details of the experimental protocol, we refer to (Liang et al., 2007)). Briefly, cells were seeded in 12-well culture plates ($20 \times 10^3$ cells per well) and grown to form a monolayer with 85\% or more confluency. Then the cell monolayer was scraped in a straight line using a pipette tip ($200 \mu L$). The debris was removed by washing with a growth medium and the medium in wells was replaced. The scratch areas were marked to obtain the same field during the image acquisition. Images of the scratches were captured immediately following the scratch formation, as well as after 24, 48 and 72 h of cultivation.
The MIMIC PERform Testing dataset contains the following physiological signals recorded from 200 critically-ill patients during routine clinical care:
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MuCeD, a dataset that is carefully curated and validated by expert pathologists from the All India Institute of Medical Science (AIIMS), Delhi, India. The H&E-stained histopathology images of the human duodenum in MuCeD are captured through an Olympus BX50 microscope at 20x zoom using a DP26 camera with each image being 1920x2148 in dimension. The dataset has 55 images, with bounding boxes for 2,090 IELs and 6,518 ENs annotated using the LabelMe software and are further validated by multiple pathologists. These cells are selected from the epithelial area -- a region of interest that has been explicitly segmented by experts. The epithelial area denotes the area of continuous villi and is used for cell detection, whereas rest of the area is masked out. Further, each image is sliced into 9 subimages and each subimage is re-scaled to 640x640, before it is given as input to object detection models. We divide 55 images into five folds of 11 images each and report 5-fold crossvalidation num
Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the original webpage)
The second Ninapro database includes 40 intact subjects and it is thoroughly described in the paper: "Manfredo Atzori, Arjan Gijsberts, Claudio Castellini, Barbara Caputo, Anne-Gabrielle Mittaz Hager, Simone Elsig, Giorgio Giatsidis, Franco Bassetto & Henning Müller. Electromyography data for non-invasive naturally-controlled robotic hand prostheses. Scientific Data, 2014" (http://www.nature.com/articles/sdata201453). Please, cite this paper for any work related to the Ninapro database. Please, use also the paper by Gijsberts et al., 2014 (http://publications.hevs.ch/index.php/publications/show/1629) for more information about the database.
Abstract The Norwegian Endurance Athlete ECG Database contains 12-lead ECG recordings from 28 elite athletes from various sports in Norway. All recordings are 10 seconds resting ECGs recorded with a General Electric (GE) MAC VUE 360 electrocardiograph. All ECGs are interpreted with both the GE Marquette SL12 algorithm (version 23 (v243)) and one cardiologist with training in interpretation of athlete's ECG. The data was collected at the University of Oslo in February and March 2020.
A total of 227 cross sectional images (20 x 54 mm with a resolution of 289 x 648 pixels) of hind-leg xenograft tumors from 29 mice were obtained with 1mm step-wise movement of the array mounted on a manual positioning device. The whole tumor volume was acquired using a diagnostic ultrasound system with a 10 MHz linear transducer and 50 MHz sampling.
Audiogram data based on a "gold standard" audiometer and the uHear iOS application of 163 participants
SinGAN-Seg-polyps is a synthetic dataset for polyp segmentation consisting of 10,000 synthetic polyps and masks.
A public open dataset of synthetic chest X-ray images of COVID-19.
A new subset of the popular open source electroencephalogram (EEG) corpus – TUH EEG: - The Temple University Artifact Corpus (TUAR) consists of high yield artifact files annotated using a five-way classification system: 1. Chewing (CHEW): An artifact resulting from the tensing and relaxing of the jaw muscles. 2. Electrode (ELEC): An artifact that encompasses various electrode related phenomena. 3. Eye Movement (EYEM): A spike-like waveform created during patient eye movement. 4. Muscle (MUSC): A common artifact with high frequency, sharp waves corresponding to patient movement. 5. Shiver (SHIV): A specific and sustained sharp wave artifact that occurs when a patient shivers. - EEG artifacts are waveforms that are not of cerebral origin and may have been affected by several external and physiological factors. - These artifacts cause false alarms in seizure prediction machine learning systems. This corpus was developed to support research and evaluation of artifact suppression technology
We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement.
Datasets at https://zenodo.org/record/8105485 for Motion Robust CMR Reconstruction Code in https://github.com/syedmurtazaarshad/motion-robust-CMR
The BCSS dataset contains over 20,000 segmentation annotations of tissue regions from breast cancer images from The Cancer Genome Atlas (TCGA). This large-scale dataset was annotated through the collaborative effort of pathologists, pathology residents, and medical students using the Digital Slide Archive. It enables the generation of highly accurate machine-learning models for tissue segmentation.
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Objective This study introduces the BlendedICU dataset, a massive dataset of international intensive care data. This dataset aims to facilitate generalizability studies of machine learning models, as well as statistical studies of clinical practices in the intensive care units.
Highlights
Dataset for the DREAMING - Diminished Reality for Emerging Applications in Medicine through Inpainting Challenge!
FHRMA is an open-source project for Fetal Heart Rate Morphological Analysis containing Matlab source code and datasets. As a sub-project, it includes a deep learning method and dataset for automatic identification of the maternal heart rate (MHR) and, more generally, false signals (FSs) on fetal heart rate (FHR) recordings. The challenge concerns particularly the FHR signal recorded with Doppler sensors, on which MHR interference and other FSs are particularly common, but the dataset also includes FHR recorded with scalp-ECG. The training and validation dataset contained 1030 expert-annotated periods (mean duration: 36 min) from 635 recordings. Labels consist of annotating each time sample as either 1: False signal; 0: True signal, or -1: do not know or irrelevant.
We've made available several genome-wide datasets, which can be used for training microRNA (miRNA) classifiers. The hairpin sequences available are from the genomes of: Homo sapiens, Arabidopsis thaliana, Anopheles gambiae, Caenorhabditis elegans and Drosophila melanogaster. Hairpin.s are small RNA sequences that naturaly folds into a hairpin-structure. However, not all hairpins have clear function (they are not miRNAs).
The medaka (Oryzias latipes) and the zebrafish (Danio rerio) are used as a model organism for a variety of subjects in biomedical research. The presented work aims to study the potential of automated ventricular dimension estimation through heart segmentation in medaka. For more on this, it's time for a closer look on our paper and the supplementary materials.
InfiniteRep is a synthetic, open-source dataset for fitness and physical therapy (PT) applications. It includes 1k videos of diverse avatars performing multiple repetitions of common exercises. It includes significant variation in the environment, lighting conditions, avatar demographics, and movement trajectories. From cadence to kinematic trajectory, each rep is done slightly differently -- just like real humans. InfiniteRep videos are accompanied by a rich set of pixel-perfect labels and annotations, including frame-specific repetition counts.
The RSNA Pulmonary Embolism CT (RSPECT) Dataset is composed of CT pulmonary angiogram images and annotations related to pulmonary embolism. It's part of the 2020 RSNA Pulmonary Embolism Detection Challenge which invited researchers to develop machine-learning algorithms to detect and characterize instances of pulmonary embolism (PE) on chest CT studies. The competition, conducted in collaboration with the Society of Thoracic Radiology (STR), involved creating the largest publicly available annotated PE dataset, comprised of more than 12,000 CT studies. Imaging data was contributed by five international research centers and labeled with detailed clinical annotations by a group of more than 80 expert thoracic radiologists. For the first time in an RSNA data challenge, the rules required competitors to submit and run their code in a standard shared environment, producing simpler, more readily usable models.
Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental de
Human activity recognition and clinical biomechanics are challenging problems in physical telerehabilitation medicine. However, most publicly available datasets on human body movements cannot be used to study both problems in an out-of-the-lab movement acquisition setting. The objective of the VIDIMU dataset is to pave the way towards affordable patient tracking solutions for remote daily life activities recognition and kinematic analysis.