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Dataset results
282 results for “image segments”
Anterior Segment Imaging With Ultrahigh-resolution OCT in Patients With Glaucoma and PEX - a Pilot Study
ClinicalTrials.gov study NCT02865473. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Reproducibility of Anterior Segment Optical Coherence Tomography (AS-OCT) for Imaging Conjunctivochalasis
ClinicalTrials.gov study NCT01933178. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Radiomics and Image Segmentation of Urinary Stones by Artificial Intelligence
ClinicalTrials.gov study NCT06412900. IPD Sharing: NO. Countries: 1. Publications: 0.
Investigator-initiated Clinical Trial to Observe Conjunctival Goblet Cell Using an Anterior Segment Imaging Device
ClinicalTrials.gov study NCT06427629. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Segmentation and intensity estimation for microarray images with saturated pixels
GEO Series GSE33899. synthetic construct; Homo sapiens. 6 samples. Type: Protein profiling by protein array.
ForTrunkSpecies - Image datasets of annotated RGB(-NIR) images for tree trunk types detection and segmentation at ground-level
<p>Two annotated image datasets for detection and segmentation of two tree trunk species - eucalyptus and pine:</p> <ul> <li>ForSpeciesDet(_4channels): dataset for tree trunk species detection in RGB(-NIR) images;</li> <li>ForSpeciesSeg(_4channels): dataset for tree trunk species segmentation in RGB(-NIR) images.</li> </ul>
Large-scale annotation dataset for cell/tissue segmentation in H&E-stained images : anti-MIST1 (plasma cells)
<p><strong>LICENSE</strong></p> <p>This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (<strong>CC-BY-NC-SA 4.0</strong>)</p> <p>For non-commercial use, please use the dataset under CC-BY-NC-SA.<br> If you would like to use the dataset for commercial purposes, please contact us (ishum-prm@m.u-tokyo.ac.jp).</p> <p>A Tar.gz file contains the following files:</p> <p>- HE image file: {antigen}_{celltype}_{slideID}_{posx}_{posy}_HE.png</p> <p>- Mask image file: {antigen}_{celltype}_{slideID}_{posx}_{posy}_mask.png</p> <p>Each image file is 984x984 px.</p> <p>posX and posY are the leftmost position in WSI coordinate.</p> <p>Mask files store binary segmentation mask (background : 0, target : 1)</p> <p> </p> <p>A csv file contains the following information:</p> <p>antigen : Antibodies for this antigen were used to create the segmentation mask.</p> <p>filename: filename of image or mask file.</p> <p>train_val_test : train, validation, or test sample in the paper.</p> <p> </p> <p><strong>Citation</strong></p> <p>If you use this dataset for your research, please cite our paper.</p> <p>Daisuke Komura, Takumi Onoyama, Koki Shinbo, Hiroto Odaka, Minako Hayakawa, Mieko Ochi, Ranny Rahaningrum Herdiantoputri, Haruya Endo, Hiroto Katoh, Tohru Ikeda, Tetsuo Ushiku, Shumpei Ishikawa,<br> Restaining-based annotation for cancer histology segmentation to overcome annotation-related limitations among pathologists, Patterns, Volume 4, Issue 2, 2023, 100688, https://doi.org/10.1016/j.patter.2023.100688.</p>
Accuracy and Reliability of Ultra Low Dose CBCT Versus CBCT Imaging in Semi-automated Segmentation of the Mandibular Condyle (A Diagnostic Accuracy Study)
ClinicalTrials.gov study NCT05441423. IPD Sharing: NO. Countries: 0. Publications: 0.
High resolution spatial trancrioptomics combined with deep learning-based image segmentation enables single-cell spatial profiling of archival FFPE kidney tissue from patients with idiopathic nephroti
GEO Series GSE300895. Homo sapiens. 3 samples. Type: Other.
Segmented RGB, LWIR, and RGB-LWIR Images of Cars and Trucks for Multispectral Automated Transfer Technique (MATT) Research
Open the record for dataset details and reuse information.
A comprehensive dataset of magnetic resonance enterography images with bowel segment annotations
<p>Inflammatory bowel disease (IBD) is a kind of recurrent bowel disease and usually requires magnetic resonance enterography (MRE) examinations for diagnosis and monitoring. However, radiologists’ recognition of bowel segments from MRE images is challenging and time-consuming. Deep learning-based medical image segmentation has shown the potential to reduce manual efforts and provide automated tools to assist in the management of disease, but it requires a large-scale fine<span>-</span>annotated dataset for training. To address this gap, we collected MRE data from 114 IBD patients. The bowel images per patient were contoured and annotated as ten segments (stomach, duodenum, small intestine, appendix, cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum), with fine pixel-level annotations labeled by experienced radiologists. Further, we <span>validated</span> the efficiency of several state-of-the-art segmentation methods on this dataset. This work established a high quality, publicly available whole bowel segment MR dataset with benchmark results and laid a groundwork for IBD’s AI research.</p>
A semantic segmentation dataset consisting of soil-root images with multiple growth stages.
<p> A semantic segmentation dataset consisting of soil-root images with multiple growth stages.</p> <blockquote> <p><strong>Last Update: 2022.08.10</strong></p> </blockquote>
Self-Supervised Learning Cell Image Dataset of Master Thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs"
<p>This is the self-supervised learning cell image dataset of master thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs". We gather images from datasets such as the LIVECell dataset, the EVICAN dataset, as well as datasets available on Image Data Resource (https://idr.openmicroscopy.org/) and the Broad Bioimage Benchmark Collection (https://bbbc.broadinstitute.org/). Only images with sizes larger than 512x512 are collected. For datasets containing more than 1000 images, we randomly select 1000 images. Otherwise, we retain all images in the dataset. </p> <p> </p> <p>After download, please put all compressed folders of subdatasets in the "image" folder under the root directory.</p>
OCTA image dataset with pixel-level mask annotation for FAZ segmentation
<p>This dataset is publish by the research "<em>A Deep Learning-based Quality Assessment and Segmentation System with a Large-scale Benchmark Dataset for Optical Coherence Tomographic Angiography Image</em>"</p> <p>Detail:</p> <p>This dataset is the pixel-level mask annotation for FAZ segmentation. 1,101 3 × 3 mm<sup>2</sup> sOCTA images chosen from gradable and best OCTA images randomly in subset sOCTA-3x3-10k, and 1,143 6 × 6 mm<sup>2</sup>dOCTA images were annotated by an experienced ophthalmologist.</p> <p>GitHub: <a href="https://github.com/shanzha09/COIPS">https://github.com/shanzha09/COIPS</a></p> <p>These datasets are public available, if you use the dataset or our system in your research, please <strong>cite</strong> our paper: <em><code>A Deep Learning-based Quality Assessment and Segmentation System with a Large-scale Benchmark Dataset for Optical Coherence Tomographic Angiography Image</code></em>.</p> <p>arXiv:<a href="https://arxiv.org/abs/2107.10476v1">https://arxiv.org/abs/2107.10476v1</a></p>
Amos: A large-scale abdominal multi-organ benchmark for versatile medical image segmentation
<p>Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. The paper can be found at https://arxiv.org/pdf/2206.08023.pdf</p> <p>In addition to providing the labeled 600 CT and MRI scans, we expect to provide 2000 CT and 1200 MRI scans without labels to support more learning tasks (semi-supervised, un-supervised, domain adaption, ...). The link can be found in:</p> <ul> <li><a href="https://zenodo.org/deposit/7262581">labeled data (500CT+100MRI)</a></li> <li><a href="https://zenodo.org/record/7262757#.Y2iSQ9JBwYs">unlabeled data Part I (900CT)</a></li> <li><a href="https://zenodo.org/record/7295661#.Y2iR_9JBwYs">unlabeled data Part II (1100CT)</a> (Now there are 1000CT, we will replenish to 1100CT)</li> <li><a href="https://zenodo.org/record/7295816">unlabeled data Part III (1200MRI)</a></li> </ul> <p>if you found this dataset useful for your research, please cite:</p> <blockquote> <pre>@inproceedings{NEURIPS2022_ee604e1b, author = {Ji, Yuanfeng and Bai, Haotian and GE, Chongjian and Yang, Jie and Zhu, Ye and Zhang, Ruimao and Li, Zhen and Zhanng, Lingyan and Ma, Wanling and Wan, Xiang and Luo, Ping}, booktitle = {Advances in Neural Information Processing Systems}, editor = {S. Koyejo and S. Mohamed and A. Agarwal and D. Belgrave and K. Cho and A. Oh}, pages = {36722--36732}, publisher = {Curran Associates, Inc.}, title = {AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation}, url = {https://proceedings.neurips.cc/paper_files/paper/2022/file/ee604e1bedbd069d9fc9328b7b9584be-Paper-Datasets_and_Benchmarks.pdf}, volume = {35}, year = {2022} } </pre> </blockquote> <p> </p>
Dataset related to the article " Automated Left and Right Ventricular Chamber Segmentation in Cardiac Magnetic Resonance Images Using Dense Fully Convolutional Neural Network"
<p>This record contains raw data related to the article " Automated left and right ventricular chamber segmentation in cardiac magnetic resonance images using dense fully convolutional neural network"</p> <p><br> Background and objective: Segmentation of the left ventricular (LV) myocardium (Myo) and RV endocardium on cine cardiac magnetic resonance (CMR) images represents an essential step for cardiacfunction evaluation and diagnosis. In order to have a common reference for comparing segmentation algorithms, several CMR image datasets were made available, but in general they do not include the most apical and basal slices, and/or gold standard tracing is limited to only one of the two ventricles, thus not fully corresponding to real clinical practice. Our aim was to develop a deep learning (DL) approach for automated segmentation of both RV and LV chambers from short-axis (SAX) CMR images, reporting separately the performance for basal slices, together with the applied criterion of choice.<br> Method: A retrospectively selected database (DB1) of 210 cine sequences (3 pathology groups) was considered: images (GE, 1.5 T) were acquired at Centro Cardiologico Monzino (Milan, Italy), and end-diastolic (ED) and end-systolic frames (ES) were manually segmented (gold standard, GS). Automatic ED and ES RV and LV segmentation were performed with a U-Net inspired architecture, where skip connections were redesigned introducing dense blocks to alleviate the semantic gap between the U-Net encoder and decoder. The proposed architecture was trained including: A) the basal slices where the Myo surrounded<br> the LV for at least the 50% and all the other slice; B) all the slices where the Myo completely surrounded the LV. To evaluate the clinical relevance of the proposed architecture in a practical use case scenario, a graphical user interface was developed to allow clinicians to revise, and correct when needed, the automatic segmentation. Additionally, to assess generalizability, analysis of CMR images obtained in 12 healthy volunteers (DB2) with different equipment (Siemens, 3T) and settings was performed.<br> Results: The proposed architecture outperformed the original U-Net. Comparing the performance on DB1 between the two criteria, no significant differences were measured when considering all slices together, but were present when only basal slices were examined. Automatic and manually-adjusted segmentation<br> performed similarly compared to the GS (bias±95%LoA): LVEDV -1±12 ml, LVESV -1±14 ml, RVEDV 6±12 ml, RVESV 6±14 ml, ED LV mass 6±26 g, ES LV mass 5±26 g). Also, generalizability showed very similar performance, with Dice scores of 0.944 (LV), 0.908 (RV) and 0.852 (Myo) on DB1, and 0.940 (LV), 0.880 (RV), and 0.856 (Myo) on DB2.<br> Conclusions: Our results support the potential of DL methods for accurate LV and RV contours segmentation and the advantages of dense skip connections in alleviating the semantic gap generated when high level features are concatenated with lower level feature. The evaluation on our dataset, considering separately the performance on basal and apical slices, reveals the potential of DL approaches for fast, accurate and reliable automated cardiac segmentation in a real clinical setting.<br> </p>
in-situ-sequencing image segmentation
Open the record for dataset details and reuse information.
The intracranial tumor segmentation challenge: ICTS 2021-unlabeled images
<p>This dataset was retrieved from clinical work of radiosurgery. It contains contrast-enhanced T1-weighted images (MRI) of 1500 patients with various brain tumors. Please see <a href="https://ntuh.ml/">https://ntuh.ml/</a> .</p>
UPOV images\Manually segmented
<p>Manually segmented images from the UPOV (International Union for the Protection of New Varieties of Plants) <em>Description of Components and Varieties of Sunflower</em> (GEVES, 2000) for determination of ray florets color.</p> <p>When using with the FloCIA software, these images should be in the folder: C:\FloCIA\Sunflowers\UPOV images\Manually segmented.</p>
Genotypes segmented images
<p>Segmented images of six ornamental sunflower genotypes that were used in the ongoing research aimed at creating new ornamental varieties in Serbia, (45.26°N, 19.83°E). Varieties : ‘Neoplanta’, ‘Heliopa’, ‘CMS1 30’, 'Ring of Fire', ‘Pacino Gold’ and ‘Dwarf’ were used for ray floret color evaluation.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.