Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
328
datasets available to search
ShareScore release 0.9.0
Dataset results
328 results for “segmentation dataset”
3D nuclei instance segmentation dataset of fluorescence microscopy volumes of C. elegans
<p>The dataset consists of 28 confocal microscopy volumes of C. elegans worms at the L1 stage and corresponding stacks of densely annotated nuclei instance segmentation masks.</p> <p>* 28 raw images and corresponding masks of average dimension (xyz) 1050 x 140 x 140<br> * Pixelsize (xyz): 0.116 x 0.116 x 0.122μm<br> * Microscope: Leica confocal microscopy, 63x oil objective</p> <p><br> The original raw data and preliminary annotations were part of the following publication (please cite if you use the dataset):<br> <br> <em>Long, F., Peng, H., Liu, X., Kim, S. K., & Myers, E. (2009). A 3D digital atlas of C. elegans and its application to single-cell analyses. Nature methods, 6(9), 667-672.</em></p> <p>The nuclei annotation masks were further manually curated by Dagmar Kainmueller (MDC Berlin) for the following publication:</p> <p><em>Hirsch, P., & Kainmueller, D. (2020). An auxiliary task for learning nuclei segmentation in 3d microscopy images. In Medical Imaging with Deep Learning (pp. 304-321). PMLR.</em></p> <p>We provide the dataset already structured into the train/validation/test split as used by the above as well as the following publications: </p> <p><em>Weigert, M., Schmidt, U., Haase, R., Sugawara, K., & Myers, G. (2020). Star-convex polyhedra for 3d object detection and segmentation in microscopy. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (pp. 3666-3673).</em><br> </p> <p> </p>
COVID Image segmentation datasets and trained model
<p>COVID CT scan datasets for segmentation and trained model for prediction created by training uNet. The referred paper is: https://www.sciencedirect.com/science/article/pii/S2666990021000069</p> <p>Origin of datasets: https://medicalsegmentation.com/covid19/</p>
Dataset for benchmarking Multiple Object Tracking and Segmentation (MOTS) in an apple orchard field.
<p>A dataset of temporally consistent apple images and labels taken using UAVs and a wearable sensor in an orchard, consisting of 86000 manually annotated apple instances and 1700 frames annotated in the MOTS (Multi-object Tracking and Segmentation) style.</p> <p>Sequence 0-5 are used for training. Sequence 6-8 are used for testing/validation. Sequence 10-12 are the testing datasets that have "ignore regions" overlays.</p> <p>The code used in the paper can be found on <a href="https://git.wur.nl/said-lab/rt-obj-tracking/">our GitLab.</a></p>
Vasculature Segmentation Validation Dataset - Part IV - Biological Difference Dataset 2/2 (Development)
<p>Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications<br> </p> <p><strong>Dataset description</strong>:</p> <p><strong>Development</strong>: Example data of the head vasculature of developing zebrafish.</p> <p><br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). </p> <p><strong>Contact</strong>: kugler.elisabeth[at]gmail.com</p> <p><strong>Useful code links</strong>: </p> <ul> <li>https://github.com/ElisabethKugler/ZFVascularQuantification</li> <li>https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis<br> </li> </ul>
Vasculature Segmentation Validation Dataset - Part III - Biological Difference Dataset 1/2 (Exsanguination)
<p>Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications</p> <p><strong>Dataset description</strong></p> <p><strong>Exsanguination</strong>: Example data of the head vasculature of 4dpf of zebrafish. Data acquisition before and after exsanguination by opening of the heart cavity with forceps in Tg(kdrl:HRAS-mCherry)s916 (4dpf; n=16 embryos from 2 experimental repeats).</p> <p><br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). </p> <p><strong>Contact</strong>: kugler.elisabeth[at]gmail.com</p> <p><strong>Useful code links</strong>: </p> <p>https://github.com/ElisabethKugler/ZFVascularQuantification<br> https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</p>
Vasculature Segmentation Validation Dataset - Part II - Decreasing Contrast-To-Noise Ratio
<p>Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications</p> <p><strong>Dataset description:</strong></p> <ul> <li><em><strong>LaserForNoise</strong></em>: Example data of the head vasculature of 4dpf of zebrafish. The data were consecutively acquired with 1.2%, 0.8%, and 0.4% laser power (LP), respectively. This allowed us to produce data with decreasing contrast-to-noise ratio, and thus study robustness over a range of signal distributions.</li> </ul> <p><em><strong>Data acquisition</strong></em>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl: HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide-semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). </p> <p><strong>Contact</strong>: kugler.elisabeth[at]gmail.com</p> <p><strong>Useful code links</strong>: </p> <ul> <li>https://github.com/ElisabethKugler/ZFVascularQuantification</li> <li>https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</li> </ul>
Vasculature Segmentation Validation Dataset - Part I - Simulated Tubes and Filter Responses
<p>Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications</p> <p><strong>Dataset description:</strong></p> <ul> <li><em><strong>SimulatedTubes</strong></em>: Computationally produced tubes (3 different sizes) that are hollow, filled, or filled with Gaussian distribution. To study filter responses, artificial noise and blurring were added.</li> <li><em><strong>DataExFilterResponse</strong></em>: Example data of the head vasculature of 4dpf of zebrafish, where the response to different filters is tested (i.e. GF - general filtering and TF - tubular filtering / Sato enhancement; for TF also different scale sizes are examined; see also: https://www.mdpi.com/2313-433X/5/1/14).</li> </ul> <p><em><strong>Data acquisition:</strong></em><br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). </p> <p><em><strong>Contact</strong></em>: kugler.elisabeth[at]gmail.com</p> <p><em><strong>Useful code links</strong></em>: </p> <ul> <li>https://github.com/ElisabethKugler/ZFVascularQuantification</li> <li>https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</li> </ul>
Tango Spacecraft Wireframe Dataset Model for Line Segments Detection
<p><strong>Reference Paper:</strong></p> <p><a href="https://doi.org/10.1016/j.actaastro.2023.01.012"><strong>M. Bechini, M. Lavagna, P. Lunghi, Dataset generation and validation for spacecraft pose estimation via monocular images processing, Acta Astronautica 204 (2023) 358–369</strong></a></p> <p><a href="https://www.researchgate.net/publication/361924362_Spacecraft_Pose_Estimation_via_Monocular_Image_Processing_Dataset_Generation_and_Validation">M. Bechini, P. Lunghi, M. Lavagna. "Spacecraft Pose Estimation via Monocular Image Processing: Dataset Generation and Validation". In 9th European Conference for Aeronautics and Aerospace Sciences (EUCASS)</a></p> <p><strong>General Description:</strong></p> <p>The "<em>Tango Spacecraft Wireframe Dataset Model for Line Segments Detection</em>" dataset here published should be used for line detection and segmentation tasks. It is split into 30002 train images and 3002 test images representing the Tango spacecraft from Prisma mission, being the only publicly available dataset of synthetic space-borne images tailored to line detection tasks (up to our knowledge). The label of each image gives the reprojection of a simplified wireframe model of Tango on the image plane split into lines. The labels are written following the Wireframe Model format. The "<em>Tango Spacecraft Wireframe Dataset Model for Line Segments Detection</em>" is also the largest dataset with wireframe annotations available up to date. More information on the dataset split and on the label format are reported below. </p> <p><strong>Images Information:</strong></p> <p>The dataset comprises 30002 synthetic grayscale images of Tango spacecraft from Prisma mission that serves as train set, while the test set is formed by 3002 synthetic grayscale images of Tango spacecraft from Prisma mission in PNG format. About 1/6 of the images both in the train and in the test set have a non-black background, obtained by rendering an Earth-like model in the raytracing process used to define the images reported. The images are noise-free to increase the flexibility of the dataset. The illumination direction of the spacecraft in the scene is uniformly distributed in the 3D space in agreement with the Sun position constraints.</p> <p><br> <strong>Labels Information:</strong></p> <p>Labels in the Wireframe dataset format are here provided in separated JSON files. The files are formatted per each image as in the following example:</p> <ul> <li> width : 98 # width in pixels (int) of the current image</li> <li> height : 176 # height in pixels (int) of the current image</li> <li> lines : [[line1], [line2], ..., [lineN]] # list of lines in each image</li> <li> filename : tango_img_866.png # string with image name and format</li> </ul> <p>Per each line (line1, ... , lineN) in lines, the format is [x0, y0, x1, y1].</p> <p>(x0, y0) are the coordinates (float) of the line starting point in the image reference frame (x pointing right and y pointing down with origin located in the top-left corner of the image).<br> (X1, y1) are the coordinates (float) of the line ending point in the image reference frame (x pointing right and y pointing down with origin located in the top-left corner of the image).</p> <p>Note that the starting point is assumed to be the left-most endpoint (lower x coordinate in image reference frame) of each line. In the case of vertical lines, the starting point is the upper-most endpoint (lower y coordinate in image reference frame) of each line.</p> <p><strong>VERSION CONTROL</strong></p> <ul> <li><strong>v1.0</strong>: All the images (both for train and test) have different resolutions, with Tango always centered in the image. The height of the images is in the range 19 - 352 pixels, while the width is in the range 16 - 336 pixels. The height over width ratio spans from 0.34 to 3.25.</li> <li><strong>v2.0</strong>: This version contains all the images of v1.0 in the .zip folder named <em>Tango_WF.zip</em>, while in the .zip folder named <em>Tango_WF_fullscale.zip</em> there is the dataset (both train and test) of full scale images. These images have width=height=1024 pixels. The position of tango with respect to the camera is randomly selected from a uniform distribution, but it is ensured the full visibility in all the images. The labels for the wireframe are in the same format of v1.0.</li> </ul> <p>Note: the dataset in v1.0 is obtained by cropping the fullscale images in v2.0 and by properly rescaling the wireframe annotations.</p> <p>Note: this dataset contains the same images of the <em>"Tango Spacecraft Dataset for Region of Interest Estimation and Semantic Segmentation</em><em>"</em> v1.0 (DOI: <a href="https://doi.org/10.5281/zenodo.6507863">https://doi.org/10.5281/zenodo.6507863</a>) and also "<em>Tango Spacecraft Dataset for Monocular Pose Estimation</em>" v1.0 (DOI: <a href="https://doi.org/10.5281/zenodo.6499007">https://doi.org/10.5281/zenodo.6499007</a>) and they can be used together by combining the annotations of the relative pose and the ones of the reprojected wireframe model of Tango, with also the ones of the ROI. <strong>These three datasets give the most comprehensive dataset of space borne synthetic images ever published</strong> (up to our knowledge).</p>
Test datasets for segmentation (2D, 3D, timelapses)
<p>Datasets for testing: 1) Arabidopsis in 3D with membrane labelling for testing Unet, Stardist and denoising models.</p> <p> 2) Ascadian embryo in 3D imaged via light sheet for testing Unet and Stardist models. </p> <p> 3) Carcinoma cells 3D + time data imaged under low SNR conditions for testing Unet, Stardist and Denoising models.</p> <p> 4) Tissue in 2D + time for testing Unet models. Data imaged by Mari Tolonen at the University of Copenhagen.</p> <p> 5) Nuclei in 3D. Raw, GT and model prediction. Data imaged by Mari Tolonen at the University of Copenhagen. </p> <p> 6) Nuclei cell mask 2D. Raw, GT and model prediction. Data imaged by Mari Tolonen at the University of Copenhagen </p>
Training dataset for "A deep learned nanowire segmentation model using synthetic data augmentation"
<p>This image dataset contains synthetic structure images used for training the deep-learning based nanowire segmentation model presented in our work "A deep learned nanowire segmentation model using synthetic data augmentation" to be published in <em>npj Computational materials. </em>Detailed information can be found in the corresponding article.</p>
Tango Spacecraft Dataset for Region of Interest Estimation and Semantic Segmentation
<p><strong>Reference Paper: </strong></p> <p><a href="https://doi.org/10.1016/j.actaastro.2023.01.012"><strong>M. Bechini, M. Lavagna, P. Lunghi, Dataset generation and validation for spacecraft pose estimation via monocular images processing, Acta Astronautica 204 (2023) 358–369</strong></a></p> <p><a href="https://www.researchgate.net/publication/361924362_Spacecraft_Pose_Estimation_via_Monocular_Image_Processing_Dataset_Generation_and_Validation">M. Bechini, P. Lunghi, M. Lavagna. "Spacecraft Pose Estimation via Monocular Image Processing: Dataset Generation and Validation". In 9th European Conference for Aeronautics and Aerospace Sciences (EUCASS)</a></p> <p><strong>General Description:</strong></p> <p>The "<em>Tango Spacecraft Dataset for Region of Interest Estimation and Semantic Segmentation</em>" dataset here published should be used for Region of Interest (ROI) and/or semantic segmentation tasks. It is split into 30002 train images and 3002 test images representing the Tango spacecraft from Prisma mission, being the largest publicly available dataset of synthetic space-borne noise-free images tailored to ROI extraction and Semantic Segmentation tasks (up to our knowledge). The label of each image gives, for the Bounding Box annotations, the filename of the image, the ROI top-left corner (minimum x, minimum y) in pixels, the ROI bottom-right corner (maximum x, maximum y) in pixels, and the center point of the ROI in pixels. The annotation are taken in image reference frame with the origin located at the top-left corner of the image, positive x rightward and positive y downward. Concerning the Semantic Segmentation, RGB masks are provided. Each RGB mask correspond to a single image in both train and test dataset. The RGB images are such that the R channel corresponds to the spacecraft, the G channel corresponds to the Earth (if present), and the B channel corresponds to the background (deep space). Per each channel the pixels have non-zero value only in correspondence of the object that they represent (Tango, Earth, Deep Space). More information on the dataset split and on the label format are reported below. </p> <p><strong>Images Information:</strong></p> <p>The dataset comprises 30002 synthetic grayscale images of Tango spacecraft from Prisma mission that serves as train set, while the test set is formed by 3002 synthetic grayscale images of Tango spacecraft from Prisma mission in PNG format. About 1/6 of the images both in the train and in the test set have a non-black background, obtained by rendering an Earth-like model in the raytracing process used to define the images reported. The images are noise-free to increase the flexibility of the dataset. The illumination direction of the spacecraft in the scene is uniformly distributed in the 3D space in agreement with the Sun position constraints.</p> <p><br> <strong>Labels Information:</strong></p> <p>Labels for the bounding box extraction are here provided in separated JSON files. The files are formatted per each image as in the following example:</p> <ul> <li> filename : tango_img_1 # name of the image to which the data are referred</li> <li> rol_tl : [x, y] # ROI top-left corner (minimum x, minimum y) in pixels</li> <li> roi_br : [x, y] # ROI bottom-right corner (maximum x, maximum y) in pixels</li> <li> roi_cc : [x, y] # center point of the ROI in pixels</li> </ul> <p>Notice that the annotation are taken in image reference frame with the origin located at the top-left corner of the image, positive x rightward and positive y downward.To make the usage of the dataset easier, both the training set and the test set are split in two folders containing the images with earth as background and without background.</p> <p>Concerning the Semantic Segmentation Labels, they are provided as RGB masks named as "filename_mask.png" where "filename" is the filename of the image of the training set or the test set to which a specific mask is referred. The RGB images are such that the R channel corresponds to the spacecraft, the G channel corresponds to the Earth (if present), and the B channel corresponds to the background (deep space). Per each channel the pixels have non-zero value only in correspondence of the object that they represent (Tango, Earth, Deep Space). </p> <p><strong>VERSION CONTROL</strong></p> <ul> <li>v1.0: This version contains the dataset (both train and test) of full scale images with ROI annotations and RGB masks for Semantic Segmentation tasks. These images have width=height=1024 pixels. The position of tango with respect to the camera is randomly selected from a uniform distribution, but it is ensured the full visibility in all the images. </li> </ul> <p>Note: this dataset contains the same images of the <em>"Tango Spacecraft Wireframe Dataset Model for Line Segments Detection"</em> v2.0 full-scale (DOI: <a href="https://doi.org/10.5281/zenodo.6372848">https://doi.org/10.5281/zenodo.6372848</a>) and also "<em>Tango Spacecraft Dataset for Monocular Pose Estimation</em>" v1.0 (DOI: <a href="https://doi.org/10.5281/zenodo.6499007">https://doi.org/10.5281/zenodo.6499007</a>) and they can be used together by combining the annotations of the relative pose and the ones of the reprojected wireframe model of Tango, with also the ones of the ROI. <strong>These three datasets give the most comprehensive dataset of space borne synthetic images ever published</strong> (up to our knowledge).</p>
Night and Day Instance Segmented Park (NDISPark) Dataset: a Collection of Images taken by Day and by Night for Vehicle Detection, Segmentation and Counting in Parking Areas
<p><strong>The Dataset</strong></p> <p>A collection of images of parking lots for <em>vehicle detection, segmentation, and counting</em>.<br> Each image is <em>manually</em> labeled with pixel-wise masks and bounding boxes localizing vehicle instances.<br> The dataset includes about 250 images depicting several parking areas describing most of the problematic situations that we can find in a real scenario: seven different cameras capture the images under various weather conditions and viewing angles. Another challenging aspect is the presence of partial occlusion patterns in many scenes such as obstacles (trees, lampposts, other cars) and shadowed cars.<br> The main peculiarity is that <em>images are taken during the day and the night</em>, showing utterly different lighting conditions.</p> <p>We suggest a three-way split (train-validation-test). The train split contains images taken during the daytime while validation and test splits include images gathered at night.<br> In line with these splits we provide some annotation files:</p> <ul> <li> <p><em>train_coco_annotations.json</em> and <em>val_coco_annotations.json</em> --> JSON files that follow the golden standard MS COCO data format (for more info see <a href="https://cocodataset.org/#format-data">https://cocodataset.org/#format-data</a>) for the training and the validation splits, respectively. All the vehicles are labeled with the COCO category<em> 'car'</em>. They are suitable for vehicle detection and instance segmentation.</p> </li> <li> <p><em>train_dot_annotations.csv</em> and <em>val_dot_annotations.csv</em> --> CSV files that contain xy coordinates of the centroids of the vehicles for the training and the validation splits, respectively. Dot annotation is commonly used for the visual counting task.</p> </li> <li> <p><em>ground_truth_test_counting.csv</em> --> CSV file that contains the number of vehicles present in each image. It is only suitable for testing vehicle counting solutions.</p> </li> </ul> <p> </p> <p><strong>Citing our work</strong></p> <p>If you found this dataset useful, please cite the following paper</p> <blockquote> <pre>@inproceedings{Ciampi_visapp_2021, doi = {10.5220/0010303401850195}, url = {https://doi.org/10.5220%2F0010303401850195}, year = 2021, publisher = {{SCITEPRESS} - Science and Technology Publications}, author = {Luca Ciampi and Carlos Santiago and Joao Costeira and Claudio Gennaro and Giuseppe Amato}, title = {Domain Adaptation for Traffic Density Estimation}, booktitle = {Proceedings of the 16th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications} } </pre> </blockquote> <p>and this Zenodo Dataset</p> <blockquote> <pre>@dataset{ciampi_ndispark_6560823, author = {Luca Ciampi and Carlos Santiago and Joao Costeira and Claudio Gennaro and Giuseppe Amato}, title = {{Night and Day Instance Segmented Park (NDISPark) Dataset: a Collection of Images taken by Day and by Night for Vehicle Detection, Segmentation and Counting in Parking Areas}}, month = may, year = 2022, publisher = {Zenodo}, version = {1.0.0}, doi = {10.5281/zenodo.6560823}, url = {https://doi.org/10.5281/zenodo.6560823} } </pre> </blockquote> <p> </p> <p><strong>Contact Information</strong></p> <p>If you would like further information about the dataset or if you experience any issues downloading files, please contact us at <a href="mailto:mobdrone@isti.cnr.it">luca.ciampi@isti.cnr.it</a></p> <p> </p>
Strawberry dataset for Semantic Segmentation
<p>The dataset was annotated using the labelme tool, and it was trained using the <a href="https://github.com/ayoolaolafenwa/PixelLib">pixellib</a>.</p> <p> </p>
Dataset for image segmentation of tree trunks from depth maps captured with a an Android app using Google ARCore
<p>This dataset consists of pairs of depth maps created with a custom-built Android app using Google's ARCore for depth estimates, and tree trunk segments obtained from depth maps captured by Huawei''s AREngine and processed with a tree diameter estimation algorithm. This dataset was used for a machine learning segmentation task that aimed to improve the inputs from ARCore tree trunk depths to the tree diameter estimation algorithm. For each pair of depth maps and segments an RGB image of the scene where samples were captured is also included.</p>
Cell-ACDC: segmentation, tracking, annotation and quantification of microscopy imaging data (dataset)
<p>This repository includes all the data generated or analysed during the preparation of Cell-ACDC publication, including test datasets for testing the software.</p> <p>Cell-ACDC is open-source software available on GitHub <a href="https://github.com/SchmollerLab/Cell_ACDC">here</a>.</p>
SOCRATES Plittersdorf Instance Segmentation Dataset
<p>A subset of video frames captured by the SOCRATES stereo camera trap in a wildlife park in Bonn, Germany between February and July of 2022, with corresponding instance segmentation annotations in the COCO format.</p>
2D Cell Instance Segmentation Dataset of Master Thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs"
<p>This is the 2D cell instance segmentation dataset of master thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs". The data is originally from the BBBC038 dataset for the Kaggle 2018 Data Science Bowl. We keep the images with annotations and the final dataset comprises 670 images in the training set and 171 images in the test set. We also converted the dataset to MSCOCO format for convenience.</p>
3D Cell Instance Segmentation Dataset of Master Thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs"
<p>This is the 3D cell instance segmentation dataset of master thesis "Enhancing Cell Instance Segmentation in 3D Microscopy using Self-Supervised ViTs". The data is originally from the BBBC027 dataset comprising 30 sets of 3D image sets with high SNR level of quality. Because only the 4 to 100 slides of every 3D image set are annotated and the main difference between annotated and unannoated slides are the brightness, to avoiding misunderstanding by the algorithms, we removed the unannotated slides and separate every slide as individual images. We also converted the dataset to MSCOCO format for convenience.</p>
Reproducible Evaluation of Open-Source Tools for Prostate Segmentation on Public Datasets
<p>Segmentation of the prostate and surrounding regions is important for a variety of clinical and research applications. Our goal is to evaluate the generalizability of publicly available state-of-the-art AI models on publicly available datasets. To compare the AI generated segmentations to the available manually annotated ground-truth, quantitative measures such as Dice Coefficient and Hausdorff distance, along with shape radiomics features, were analyzed. Our study also aims to show how cloud-based tools can be used to analyze, store, and visualize evaluation results.<strong> </strong></p> <p>Three open-source pre-trained AI prostate segmentation tools were evaluated against expert annotations, on three publicly available MRI prostate collections, available in NCI Imaging Data Commons[1]. Two pre-trained models originate from the nnU-Net framework[2], the last pre-trained model originates from Prostate158 paper[4]. ProstateX[5], QIN-Prostate-Repeatability[6] and PROSTATE-MRI-US-Biopsy[7]. Expert annotations of the the whole prostate gland, peripheral zone (PZ) and transition zone (TZ) of the prostate are available for ProstateX collection, whole prostate gland and PZ for QIN-Prostate-Repeatability collection, and whole prostate gland for PROSTATE-MRI-US-Biopsy collection.</p> <p>We rely on the DICOM standard to encode our segmentation and radiomics results. The DICOM standard aims to achieve interoperability and FAIR[10] principles. Encoding our results in DICOM representation allows us to leverage DICOM-reliant tools, such as Google Cloud Computing tools for storage,computation, analysis and visualization. Open-source DICOM-based visualization tools such as OHIF[8] viewer can also be used to look qualitatively at the AI and expert annotations and the referenced images.. DICOM Segmentation objects are used to encode the AI models predictions, using dcmqi[11], DICOM Structured Reports on the other hand are used to encode radiomics features[3] extracted from the AI and expert annotations, using dcmqi and highdicom[12]. </p> <p>This dataset is organized in three parts: </p> <p>AI_SEGMENTATIONS_DICOM.zip, AI_STRUCTURED_REPORTS_DICOM.zip and EXPERT_SRUCTURED_REPORTS_DICOM..zip. All zip files contain DICOM objects only, sorted based on DICOM attributes, following this pattern:</p> <p>PatientID/<br> └───Modality-%StudyInstanceUID/<br> └───%SeriesInstanceUID-%SeriesDescription.dcm.</p> <p>AI_SEGMENTATIONS_DICOM.zip contains all the pre-trained AI models evaluated segmentation results, encoded as DICOM Segmentation objects. AI_STRUCTURED_REPORTS_DICOM..zip contains firstorder and shape radiomics features extracted for the AI segmentation results, such as Segmentation Volume, encoded as DICOM Structured Reports. EXPERT_SRUCTURED_REPORTS_DICOM.zip contains firstorder and shape radiomics features extracted for the expert annotations (for ProstateX, QIN-Prostate-Repeatability and PROSTATE-MRI-US-Biopsy collections) stored a DICOM Structured Reports objects.</p> <p>Code repository containing evaluation cloud-based notebooks and results/metadata .csv tables is available here:<br><a href="https://github.com/ImagingDataCommons/idc-prostate-mri-analysis">https://github.com/ImagingDataCommons/idc-prostate-mri-analysis</a></p> <h2>Additional Notes</h2> <p><strong> </strong>This project has been funded in whole or in part with Federal funds from the NCI, NIH, under task order no. HHSN26110071 under contract no. HHSN261201500003l.<br>https://portal.imaging.datacommons.cancer.gov/</p> <p>nnU-Net: <a href="https://github.com/MIC-DKFZ/nnUNet">https://github.com/MIC-DKFZ/nnUNet</a> <br>Prostate158: <a href="https://github.com/Project-MONAI/model-zoo/tree/dev/models/prostate_mri_anatomy">https://github.com/Project-MONAI/model-zoo/tree/dev/models/prostate_mri_anatomy</a><br>Pyradiomics: <a href="https://github.com/AIM-Harvard/pyradiomics">https://github.com/AIM-Harvard/pyradiomics</a> <br>Highdicom: <a href="https://github.com/herrmannlab/highdicom">https://github.com/herrmannlab/highdicom</a> <br>DCMQI: <a href="https://github.com/QIICR/dcmqi">https://github.com/QIICR/dcmqi</a> <br>Github repo: <a href="https://github.com/ImagingDataCommons/idc-prostate-mri-analysis">https://github.com/ImagingDataCommons/idc-prostate-mri-analysis</a></p> <h2>Related information</h2> <p>ProstateX - <a href="https://doi.org/10.7937/K9TCIA.2017.MURS5CL">https://doi.org/10.7937/K9TCIA.2017.MURS5CL </a><br><br>QIN-Prostate-Repeatability - <a href="https://doi.org/10.7937/K9/TCIA.2018.MR1CKGND">https://doi.org/10.7937/K9/TCIA.2018.MR1CKGND</a><br><br>PROSTATE-MRI-US-BIOPSY - <a href="https://doi.org/10.7937/TCIA.2020.A61IOC1A">https://doi.org/10.7937/TCIA.2020.A61IOC1A</a></p> <h2>References </h2> <p>[1] Fedorov A, Longabaugh WJ, Pot D, Clunie DA, Pieper S, Aerts HJ, Homeyer A, Lewis R, Akbarzadeh A, Bontempi D, Clifford W. NCI imaging data commons. Cancer research. 2021 Aug 8;81(16):4188.</p> <p>[2] Isensee F, Jaeger PF, Kohl SA, Petersen J, Maier-Hein KH. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature methods. 2021 Feb;18(2):203-11.</p> <p>[3] Van Griethuysen JJ, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V, Beets-Tan RG, Fillion-Robin JC, Pieper S, Aerts HJ. Computational radiomics system to decode the radiographic phenotype. Cancer research. 2017 Nov 1;77(21):e104-7.</p> <p>[4] Adams, Lisa C., Marcus R. Makowski, Günther Engel, Maximilian Rattunde, Felix Busch, Patrick Asbach, Stefan M. Niehues, et al. 2022. “Prostate158 - An Expert-Annotated 3T MRI Dataset and Algorithm for Prostate Cancer Detection.” Computers in Biology and Medicine 148 (September): 105817.</p> <p>[5] Natarajan, S., Priester, A., Margolis, D., Huang, J., & Marks, L. (2020). Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy) (version 2) [Data set]. The Cancer Imaging Archive. DOI: 10.7937/TCIA.2020.A61IOC1A</p> <p>[6] Fedorov, A; Schwier, M; Clunie, D; Herz, C; Pieper, S; Kikinis, R; Tempany, C; Fennessy, F. (2018). Data From QIN-PROSTATE-Repeatability. The Cancer Imaging Archive. DOI: 10.7937/K9/TCIA.2018.MR1CKGND</p> <p>[7] Natarajan, S., Priester, A., Margolis, D., Huang, J., & Marks, L. (2020). Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy) (version 2) [Data set]. The Cancer Imaging Archive. DOI: 10.7937/TCIA.2020.A61IOC1A</p> <p>[8] Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research. Erik Ziegler, Trinity Urban, Danny Brown, James Petts, Steve D. Pieper, Rob Lewis, Chris Hafey, and Gordon J. Harris</p> <p>[9] Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L. The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository. Journal of digital imaging. 2013 Dec;26(6):1045-57.</p> <p>[10] Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J. The FAIR Guiding Principles for scientific data management and stewardship. Scientific data. 2016 Mar 15;3(1):1-9.</p> <p>[11] Herz C, Fillion-Robin JC, Onken M, Riesmeier J, Lasso A, Pinter C, Fichtinger G, Pieper S, Clunie D, Kikinis R, Fedorov A. DCMQI: an open source library for standardized communication of quantitative image analysis results using DICOM. Cancer research. 2017 Nov 1;77(21):e87-90.</p> <p>[12] Bridge CP, Gorman C, Pieper S, Doyle SW, Lennerz JK, Kalpathy-Cramer J, Clunie DA, Fedorov AY, Herrmann MD. Highdicom: A python library for standardized encoding of image annotations and machine learning model outputs in pathology and radiology. Journal of Digital Imaging. 2022 Aug 22:1-9.</p> <p> </p>
Dataset for Interspeech 2018 submission: Singing voice phoneme segmentation by hierarchically inferring syllable and phoneme onset positions
<p>This dataset contains the materials for training, testing the joint and HSMM models mentioned in the paper "<em>Singing voice phoneme segmentation by hierarchically inferring syllable and phoneme onset positions"</em>.</p> <p>The filename list of this dataset can be found in the function <em>get_train_test_recordings_joint()</em> of <em>./general/trainTestSeparation.py</em> file. The dataset contains the Praat TextGrids and .wavs of the variables: <em>train_primary_school, val_primary_school</em> and <em>test_primary_school</em>. For accessing other datasets such as <em>train_nacta_2017, train_nacta</em> and <em>train_sepa</em>, please download them from the links:</p> <p>jingju dataset part1: <a href="https://zenodo.org/record/1185154">https://zenodo.org/record/1185154</a></p> <p>jingju dataset part2: <a href="https://doi.org/10.5281/zenodo.842229">https://doi.org/10.5281/zenodo.842229</a></p> <p>Once you have downloaded these three datasets, you need to set the paths in <em>./general/filePathShared.py</em>.</p> <p>Set <em>path_jingju_dataset</em> to the parent path of these three datasets.</p> <p>Set <em>primarySchool_dataset_root_path</em> to the path of the interspeech2018 dataset (the current dataset).</p> <p>Set <em>nacta_dataset_root_path</em> to the path of the jingju dataset part1.</p> <p>Set <em>nacta2017_dataset_root_path</em> to the path the jingju dataset part2.</p> <p>For more information on this paper, please refer to the Github page: <a href="https://github.com/ronggong/interspeech2018_submission01">https://github.com/ronggong/interspeech2018_submission01</a></p> <p> </p>
ScienceDex guides
Understand access before you commit
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.