The OME-Zarr Open SciVis Datasets project provides the Open SciVis Dataset in a chunked, multi-scale format, encodes metadata in JSON according to the OME-Zarr specification, and hosts the datasets on AWS S3 through the AWS Open Data Program, aiming to serve as a web-based resource for the scientific visualization community to enhance reproducibility and facilitate testing and development of OME-Zarr tools.
OME-Zarr is a cloud-optimized bioimaging file format that has emerged as a promising solution to address the challenges of scalability and heterogeneity in scientific data exchange. Developed by the Open Microscopy Environment (OME) in collaboration with an international community of researchers and institutions, OME-Zarr builds upon the Zarr format to provide a flexible and scalable method for storing multidimensional imaging data and associated metadata.
The format is designed to support both pixel measurements and relevant imaging metadata, including experimental, acquisition, and analytic information. OME-Zarr offers significant advantages over traditional formats like TIFF and HDF5, particularly in its ability to efficiently handle large, multi-Gigabyte to Petabyte datasets in cloud-based storage environments. By storing data in individually referenceable "chunk" files, OME-Zarr enables fast, random access to specific portions of large datasets without requiring access to the entire file.
Since its initial publication in 2021, OME-Zarr has seen rapid adoption and expansion of supporting tools. The format now accommodates a wide range of bioimaging modalities and derived data types, such as regions of interest (ROIs) and segmentation labels. This growth has been driven by an open, collaborative development process that brings together diverse use cases and requirements from across the bioimaging community. As a result, OME-Zarr is emerging as a unifying format that promotes FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in the bioimaging domain, facilitating more efficient data management, analysis, and sharing across personal, institutional, and global scales.
For more information about OME-Zarr, including the latest specifications, reference implementations, and community resources, please visit the OME-Zarr website, including the reference publications and the format specification.
The Open SciVis Datasets, curated by Pavol Klacansky, is a valuable resource for the scientific visualization community. This collection provides a diverse range of volumetric datasets that are freely available for use in research, education, and development of visualization techniques.
The datasets span various scientific domains, including medical imaging, fluid dynamics, astrophysics, and materials science. Each dataset is provided in a standardized format, typically raw binary files accompanied by metadata describing dimensions, data types, and other relevant information.
One of the key benefits of this collection is that it offers high-quality, real-world datasets that can be used to test and benchmark visualization algorithms and software. This is particularly useful for researchers and developers working on volume rendering, isosurface extraction, transfer function design, and other visualization techniques.
The Open SciVis Datasets website provides easy access to download the datasets, along with previews and descriptions of each dataset's contents and origins. This makes it simple for users to find appropriate datasets for their specific needs or interests.
By making these datasets freely available, Klacansky's collection promotes reproducibility in scientific visualization research and enables fair comparisons between different visualization methods using common benchmark data.
The OME-Zarr Open SciVis Datasets project is an innovative initiative that brings together two valuable resources for the scientific visualization community: the Open SciVis Datasets curated by Pavol Klacansky and the OME-Zarr file format developed by the Open Microscopy Environment.
This project takes the original Open SciVis Datasets and converts them into the OME-Zarr format, providing several key enhancements:
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The datasets are restructured into a chunked, multi-scale form, allowing for efficient access to different resolutions and subsets of the data.
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Metadata for each dataset is encoded in JSON format according to the OME-Zarr specification, providing standardized and machine-readable information about the data's structure and properties.
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The converted datasets are hosted on Amazon Web Services (AWS) S3 through the AWS Open Data Program, ensuring wide accessibility and scalability.
The primary aim of the OME-Zarr Open SciVis Datasets project is to create a web-based resource that serves the scientific visualization community in multiple ways:
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It promotes reproducibility in research by providing standardized, easily accessible datasets that can be used as benchmarks or test cases across different studies.
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It offers a rich dataset resource for developers working on OME-Zarr tools, allowing them to test and refine their implementations using real-world scientific data.
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It demonstrates the capabilities of the OME-Zarr format in handling diverse types of scientific visualization data, from medical imaging to fluid dynamics simulations.
By combining the high-quality datasets from the Open SciVis collection with the advanced features of the OME-Zarr format, this project aims to accelerate progress in scientific visualization research and tool development while fostering greater interoperability and data sharing within the community.
Rotational C-arm x-ray scan of the arteries of the right half of a human head. A contrast agent was injected into the blood and an aneurism is present.
Details
Dataset Name: aneurism
Dataset Type: uint8
Dataset Size: [256, 256, 256]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/aneurism.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/aneurism.ome.zarr
Acknowledgement: volvis.org and Philips Research, Hamburg, Germany
CT scan of a backpack filled with items.
Details
Dataset Name: backpack
Dataset Type: uint16
Dataset Size: [512, 512, 373]
Dataset Spacing: [0.9766, 0.9766, 1.25]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/backpack.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/backpack.ome.zarr
Acknowledgement: volvis.org and Kevin Kreeger, Viatronix Inc., USA
A microCT scan of a dried beechnut.
Details
Dataset Name: beechnut
Dataset Type: uint16
Dataset Size: [1024, 1024, 1546]
Dataset Spacing: [2e-05, 2e-05, 2e-05]
Dataset Scales: 5
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/beechnut.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/beechnut.ome.zarr
Acknowledgement: The Computer-Assisted Paleoanthropology group and the Visualization and MultiMedia Lab at University of Zurich (UZH)
Details
Dataset Name: blunt_fin
Dataset Type: uint8
Dataset Size: [256, 128, 64]
Dataset Spacing: [1, 0.75, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/blunt_fin.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/blunt_fin.ome.zarr
Acknowledgement: NASA Advanced Supercomputing Division, USA
CT scan of a bonsai tree.
Details
Dataset Name: bonsai
Dataset Type: uint8
Dataset Size: [256, 256, 256]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/bonsai.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/bonsai.ome.zarr
Acknowledgement: volvis.org and S. Roettger, VIS, University of Stuttgart
CT scan of the SIGGRAPH 1989 teapot with a small version of the AVS lobster inside.
Details
Dataset Name: boston_teapot
Dataset Type: uint8
Dataset Size: [256, 256, 178]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/boston_teapot.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/boston_teapot.ome.zarr
Acknowledgement: volvis.org and Terarecon Inc, MERL, Brigham and Women's Hospital
A CT scan of the Stanford Bunny. The greyscale units are Hounsfield units, denoting electron-density of the subject; the scale units are in millimeters. The scan was completed 28 January 2000.
Details
Dataset Name: bunny
Dataset Type: uint16
Dataset Size: [512, 512, 361]
Dataset Spacing: [0.337891, 0.337891, 0.5]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/bunny.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/bunny.ome.zarr
Acknowledgement: Many many thanks to Geoff Rubin who helped me to scan the data, Sandy Napel who coordinated the scan and helped to process the data, and Marc Levoy who graciously provided the subject. Geoff and Sandy are with Stanford Radiology, and Marc is with Stanford Computer Science.
CT scan of a carp fish
Details
Dataset Name: carp
Dataset Type: uint16
Dataset Size: [256, 256, 512]
Dataset Spacing: [0.78125, 0.390625, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/carp.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/carp.ome.zarr
Acknowledgement: Michael Scheuring, Computer Graphics Group, University of Erlangen, Germany
CT scan of a chameleon.
Details
Dataset Name: chameleon
Dataset Type: uint16
Dataset Size: [1024, 1024, 1080]
Dataset Spacing: [0.09228515625, 0.09228515625, 0.105]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/chameleon.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/chameleon.ome.zarr
Acknowledgement: Chamaeleo calyptratus. Digital Morphology, 2003.
The Christmas tree model was scanned with a Siemens Somatom Plus 4 Volume Zoom Multislice-CT scanner at the general hospital in Vienna.
Details
Dataset Name: christmas_tree
Dataset Type: uint16
Dataset Size: [512, 499, 512]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/christmas_tree.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/christmas_tree.ome.zarr
Acknowledgement: Armin Kanitsar, 2002
A single time step from a computational simulation of a jet of heptane gas undergoing combustion.
Details
Dataset Name: csafe_heptane
Dataset Type: uint8
Dataset Size: [302, 302, 302]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/csafe_heptane.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/csafe_heptane.ome.zarr
Acknowledgement: The University of Utah Center for the Simulation of Accidental Fires and Explosions.
A wall-bounded flow in a duct.
Details
Dataset Name: duct
Dataset Type: float32
Dataset Size: [193, 194, 1000]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/duct.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/duct.ome.zarr
Acknowledgement: Marco Atzori, Ricardo Vinuesa, Adrián Lozano-Durán, and Philipp Schlatter. This work was supported by grants from the Swedish Foundation for Strategic Research, project “In-Situ Big Data Analysis for Flow and Climate Simulations” (Ref. number BD15-0082) and from the Knut and Alice Wallenberg Foundation. The simulation were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC).
CT scan of two cylinders of an engine block.
Details
Dataset Name: engine
Dataset Type: uint8
Dataset Size: [256, 256, 128]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/engine.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/engine.ome.zarr
Acknowledgement: volvis.org and General Electric
Rotational C-arm x-ray scan of a human foot. Tissue and bone are present in the dataset.
Details
Dataset Name: foot
Dataset Type: uint8
Dataset Size: [256, 256, 256]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/foot.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/foot.ome.zarr
Acknowledgement: volvis.org and Philips Research, Hamburg, Germany
MRI scan of a frog as part of the Whole Frog Project.
Details
Dataset Name: frog
Dataset Type: uint8
Dataset Size: [256, 256, 44]
Dataset Spacing: [0.5, 0.5, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/frog.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/frog.ome.zarr
Acknowledgement: Lawrence Berkeley Laboratory, USA
Simulation of fuel injection into a combustion chamber. The higher the density value, the less presence of air.
Details
Dataset Name: fuel
Dataset Type: uint8
Dataset Size: [64, 64, 64]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/fuel.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/fuel.ome.zarr
Acknowledgement: volvis.org and SFB 382 of the German Research Council (DFG)
The first timestep of direct numerical simulation of an autoignition phenomena in stratified dimethyl-ether/air turbulent mixtures.
Details
Dataset Name: hcci_oh
Dataset Type: float32
Dataset Size: [560, 560, 560]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/hcci_oh.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/hcci_oh.ome.zarr
Acknowledgement: Gaurav Bansal, Ajith Mascarenhas, and Jacqueline H. Chen.
Simulation of the spatial probability distribution of the electron in an hydrogen atom, residing in a strong magnetic field.
Details
Dataset Name: hydrogen_atom
Dataset Type: uint8
Dataset Size: [128, 128, 128]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/hydrogen_atom.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/hydrogen_atom.ome.zarr
Acknowledgement: volvis.org and SFB 382 of the German Research Council (DFG)
Q-criterion of a jet in crossflow created by a direct numerical simulation.
Details
Dataset Name: jicf_q
Dataset Type: float32
Dataset Size: [1408, 1080, 1100]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/jicf_q.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/jicf_q.ome.zarr
Acknowledgement: Computational support and resources were provided by the National Center for Computational Sciences at Oak Ridge National Laboratory, which is supported by the Office of Science of the US Department of Energy under contract DE-AC05-00OR22725. The work at NREL was supported by the US Department of Energy under contract DE-AC36-08-GO28308 with the National Renewable Energy Laboratory. The work at Sandia National Laboratories was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy and by the US Department of Energy SciDAC Program. SNL is a multiprogramme laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the US DOE under contract DE-AC04-94AL85000. The work at SINTEF was produced with support from Gassnova through the BIGH2/SP2 project and from the BIGCCS Centre, performed under the Norwegian research programme Centres for Environment-Friendly Energy Research (FME). The authors acknowledge the following partners for their contributions: Aker Solutions, ConocoPhillips, Det Norske Veritas, Gassco, Hydro, Shell, Statoil, TOTAL, GDF SUEZ and the Research Council of Norway (193816/S60).
Scan of a Lampropeltis getula egg (captive bred by Travis LaDuc; laid on 7 July 2003, growth terminated on 29 August 2003, 54 days after oviposition) for Dr. Timothy Rowe of the Department of Geological Sciences, The University of Texas at Austin.
Details
Dataset Name: kingsnake
Dataset Type: uint8
Dataset Size: [1024, 1024, 795]
Dataset Spacing: [0.03174, 0.03174, 0.0688]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/kingsnake.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/kingsnake.ome.zarr
Acknowledgement: DigiMorph.org, The University of Texas High-Resolution X-ray CT Facility (UTCT), and NSF grant IIS-9874781
CT scan of a lobster contained in a block of resin.
Details
Dataset Name: lobster
Dataset Type: uint8
Dataset Size: [301, 324, 56]
Dataset Spacing: [1, 1, 1.4]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/lobster.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/lobster.ome.zarr
Acknowledgement: volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA
A single time step from a computational simulation of magnetic reconnection.
Details
Dataset Name: magnetic_reconnection
Dataset Type: float32
Dataset Size: [512, 512, 512]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/magnetic_reconnection.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/magnetic_reconnection.ome.zarr
Acknowledgement: Bill Daughton (LANL) and Berk Geveci (KitWare). Please acknowledge paper http://arxiv.org/abs/1405.4040.
Pyramidal neurons in the marmoset primary visual cortex (V1) labeled with green fluorescent protein (GFP) after injection of a psuedotyped G-deleted rabies virus in area V2. The tissue was cleared using the Sca/e technique and imaged on a Olympus 2-photon microscope at 20x magnification.
Details
Dataset Name: marmoset_neurons
Dataset Type: uint8
Dataset Size: [1024, 1024, 314]
Dataset Spacing: [0.497, 0.497, 1.5]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/marmoset_neurons.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/marmoset_neurons.ome.zarr
Acknowledgement: Frederick Federer, Moran Eye Institute, University of Utah
High frequencies where 99% of the sinusoids are right below the Nyquist frequency.
Details
Dataset Name: marschner_lobb
Dataset Type: uint8
Dataset Size: [41, 41, 41]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/marschner_lobb.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/marschner_lobb.ome.zarr
Acknowledgement: volvis.org and Marschner and Lobb
A time step of a density field in a simulation of the mixing transition in Rayleigh-Taylor instability.
Details
Dataset Name: miranda
Dataset Type: float32
Dataset Size: [1024, 1024, 1024]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/miranda.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/miranda.ome.zarr
Acknowledgement: Andrew W. Cook, William Cabot, and Paul L. Miller
1.5T MRT 3D CISS dataset of a human head that highlights the CSF (Cerebro-Spinal-Fluid) filled cavities of the head.
Details
Dataset Name: mri_ventricles
Dataset Type: uint8
Dataset Size: [256, 256, 124]
Dataset Spacing: [0.9, 0.9, 0.9]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/mri_ventricles.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/mri_ventricles.ome.zarr
Acknowledgement: volvis.org and Dirk Bartz, VCM, University of Tübingen, Germany
MRI scan of a woman's head
Details
Dataset Name: mri_woman
Dataset Type: uint16
Dataset Size: [256, 256, 109]
Dataset Spacing: [1, 1, 1.5]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/mri_woman.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/mri_woman.ome.zarr
Acknowledgement: Siemens Medical Systems, Inc., Iselin, NJ., USA
3T MRT Time-of-Flight Angiography dataset of a human head. The dataset has been resampled into an isotropic voxel grid (hence the peculiar slice size).
Details
Dataset Name: mrt_angio
Dataset Type: uint16
Dataset Size: [416, 512, 112]
Dataset Spacing: [0.412, 0.412, 0.412]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/mrt_angio.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/mrt_angio.ome.zarr
Acknowledgement: volvis.org and Özlem Gürvit, Institute for Neuroradiology, Frankfurt, Germany
Simulation of the spatial probability distribution of the electrons in a high potential protein molecule.
Details
Dataset Name: neghip
Dataset Type: uint8
Dataset Size: [64, 64, 64]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/neghip.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/neghip.ome.zarr
Acknowledgement: volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA
Axons in layer 1 of the mouse barrel cortex imaged in vivo.
Details
Dataset Name: neocortical_layer_1_axons
Dataset Type: uint8
Dataset Size: [1464, 1033, 76]
Dataset Spacing: [1, 1, 3.4]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/neocortical_layer_1_axons.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/neocortical_layer_1_axons.ome.zarr
Acknowledgement: V De Paola, MRC Clinical Sciences Center, Imperial College London
Simulation of the two-body distribution probability of a nucleon in the atomic nucleus 16O if a second nucleon is known to be positioned at r'=(2 fm,0,0).
Details
Dataset Name: nucleon
Dataset Type: uint8
Dataset Size: [41, 41, 41]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/nucleon.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/nucleon.ome.zarr
Acknowledgement: volvis.org and SFB 382 of the German Research Council (DFG)
First scan. The National Institutes of Health Clinical Center performed 82 abdominal contrast enhanced 3D CT scans (~70 seconds after intravenous contrast injection in portal-venous) from 53 male and 27 female subjects. Seventeen of the subjects are healthy kidney donors scanned prior to nephrectomy. The remaining 65 patients were selected by a radiologist from patients who neither had major abdominal pathologies nor pancreatic cancer lesions. Subjects' ages range from 18 to 76 years with a mean age of 46.8 ± 16.7. The CT scans have resolutions of 512x512 pixels with varying pixel sizes and slice thickness between 1.5 - 2.5 mm, acquired on Philips and Siemens MDCT scanners (120 kVp tube voltage). A medical student manually performed slice-by-slice segmentations of the pancreas as ground-truth and these were verified/modified by an experienced radiologist.
Details
Dataset Name: pancreas
Dataset Type: int16
Dataset Size: [240, 512, 512]
Dataset Spacing: [1.16, 1.0, 1.0]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/pancreas.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/pancreas.ome.zarr
Acknowledgement: Roth HR, Lu L, Farag A, Shin H-C, Liu J, Turkbey EB, Summers RM. DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation. N. Navab et al. (Eds.): MICCAI 2015, Part I, LNCS 9349, pp. 556-564, 2015.
This specimen, the holotype, was collected from the Paw Paw Formation, SMU Loc. No. 263, Tarrant County, Texas. The specimen was scanned along the coronal axis for a total of 1088 slices. Voxel size is 0.2275 mm.
Details
Dataset Name: pawpawsaurus
Dataset Type: uint16
Dataset Size: [958, 646, 1088]
Dataset Spacing: [0.2275, 0.2275, 0.2275]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/pawpawsaurus.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/pawpawsaurus.ome.zarr
Acknowledgement: Matthew Colbert, 4 February 2014
Volumes were obtained by way of computed tomography (CT) imaging on excised, postmortem porcine hearts. Alginate curing agents were injected into ventricles to provide rigidity and radiopaque agents were injected into the coronary arteries to distinguish microvasculature from the rest of the tissue.
Details
Dataset Name: pig_heart
Dataset Type: int16
Dataset Size: [2048, 2048, 2612]
Dataset Spacing: [0.03557, 0.03557, 0.03557]
Dataset Scales: 5
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/pig_heart.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/pig_heart.ome.zarr
Acknowledgement: Experiments were performed by the Cardiovascular Research and Training Institute (CVRTI) and the Scientific Computing and Imaging (SCI) Institute at the University of Utah with funding from the Nora Eccles Treadwell foundation and the NIH/NIGMS Center of Integrative Biomedical Computing under grant P41 GM103545-17.
An industrial CT scan of a christmas present.
Details
Dataset Name: present
Dataset Type: uint16
Dataset Size: [492, 492, 442]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/present.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/present.ome.zarr
Acknowledgement: Christoph Heinzl, 2006
CT scan of abdomen in prone orientation (back faces ceiling, belly faces table).
Details
Dataset Name: prone
Dataset Type: uint16
Dataset Size: [512, 512, 463]
Dataset Spacing: [0.625, 0.625, 1.0]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/prone.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/prone.ome.zarr
Acknowledgement: volvis.org and Walter Reed Army Medical Center, USA
Entropy field (timestep 160) of Richtmyer-Meshkov instability simulation.
Details
Dataset Name: richtmyer_meshkov
Dataset Type: uint8
Dataset Size: [2048, 2048, 1920]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 5
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/richtmyer_meshkov.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/richtmyer_meshkov.ome.zarr
Acknowledgement: Three-dimensional simulation of a Richtmyer-Meshkov instability with a two-scale initial perturbation, Ronald H. Cohen, William P. Dannevik, Andris M. Dimits, Donald E. Eliason, Arthur A. Mirin, and Ye Zhou
Simulation of an unsteady interaction of a planar shockwave with a randomly-perturbed contact discontinuity.
Details
Dataset Name: shockwave
Dataset Type: uint8
Dataset Size: [64, 64, 512]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/shockwave.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/shockwave.ome.zarr
Acknowledgement: volvis.org
Simulation of a silicium grid.
Details
Dataset Name: silicium
Dataset Type: uint8
Dataset Size: [98, 34, 34]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/silicium.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/silicium.ome.zarr
Acknowledgement: volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA
Rotational C-arm x-ray scan of phantom of a human skull.
Details
Dataset Name: skull
Dataset Type: uint8
Dataset Size: [256, 256, 256]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/skull.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/skull.ome.zarr
Acknowledgement: volvis.org and Siemens Medical Solutions, Forchheim, Germany
This specimen, the holotype, was collected from the Middle Eocene Green River Formation of Sweetwater County, Wyoming on 27 July 1967 by Frank L. Pearce. The specimen was scanned along the coronal axis for a total of 750 slices. Each 1024x1024 pixel slice is 0.047 mm thick, with an interslice spacing of 0.047 mm and a field of reconstruction of 22 mm.
Details
Dataset Name: spathorhynchus
Dataset Type: uint16
Dataset Size: [1024, 1024, 750]
Dataset Spacing: [0.0215, 0.0215, 0.047]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/spathorhynchus.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/spathorhynchus.ome.zarr
Acknowledgement: Matthew Colbert, 17 February 2005
The stag beetle from Georg Glaeser, Vienna University of Applied Arts, Austria, was scanned with an industrial CT by Johannes Kastner, Wels College of Engineering, Austria, and Meister Eduard Gröller, Vienna University of Technology, Austria.
Details
Dataset Name: stag_beetle
Dataset Type: uint16
Dataset Size: [832, 832, 494]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/stag_beetle.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/stag_beetle.ome.zarr
Acknowledgement: Meister Eduard Gröller, Georg Glaeser, Johannes Kastner, 2005
CT scan of a leg of a bronze statue.
Details
Dataset Name: statue_leg
Dataset Type: uint8
Dataset Size: [341, 341, 93]
Dataset Spacing: [1, 1, 4]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/statue_leg.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/statue_leg.ome.zarr
Acknowledgement: volvis.org and German Federal Institute for Material Research and Testing (BAM), Berlin, Germany
CT Scan of the abdomen and pelvis. The dataset contains also a stent in the abdominal aorta. No contrast agent was used to enhance the blood vessels.
Details
Dataset Name: stent
Dataset Type: uint16
Dataset Size: [512, 512, 174]
Dataset Spacing: [0.8398, 0.8398, 3.2]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/stent.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/stent.ome.zarr
Acknowledgement: volvis.org and Michael Meißner, Viatronix Inc., USA
A simulated CT scan of a 8x8x8 octet truss with five defects on the front side of the object. The defects are bent strut, broken strut, missing strut, dross, and thin strut.
Details
Dataset Name: synthetic_truss_with_five_defects
Dataset Type: float32
Dataset Size: [1200, 1200, 1200]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 4
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/synthetic_truss_with_five_defects.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/synthetic_truss_with_five_defects.ome.zarr
Acknowledgement: The CAD meshes can be found here https://data-science.llnl.gov/open-data-initiative. The dataset is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License. Copyright (c) 2022, Lawrence Livermore National Security, LLC. Produced at the Lawrence Livermore National Laboratory. Written by Haichao Miao. Release number - LLNL-MISC-833578. All rights reserved. This work was produced under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. This work was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor Lawrence Livermore National Security, LLC, nor any of their employees makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or Lawrence Livermore National Security, LLC. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or Lawrence Livermore National Security, LLC, and shall not be used for advertising or product endorsement purposes.
The dataset represents a time step from an isotropic turbulence simulation. A single variable, enstrophy, is represented on a Cartesian grid.
Details
Dataset Name: tacc_turbulence
Dataset Type: float32
Dataset Size: [256, 256, 256]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/tacc_turbulence.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/tacc_turbulence.ome.zarr
Acknowledgement: Dataset provided by Gregory D. Abram and Gregory P. Johnson, Texas Advanced Computing Center, The University of Texas at Austin. Simulation by Diego A. Donzis, Texas A&M University, P.K. Yeung, Georgia Tech.
Details
Dataset Name: tooth
Dataset Type: uint8
Dataset Size: [103, 94, 161]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 1
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/tooth.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/tooth.ome.zarr
Acknowledgement:
Rotational angiography scan of a head with an aneurysm. Only contrasted blood vessels are visible.
Details
Dataset Name: vertebra
Dataset Type: uint16
Dataset Size: [512, 512, 512]
Dataset Spacing: [0.1953, 0.1953, 0.1953]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/vertebra.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/vertebra.ome.zarr
Acknowledgement: volvis.org and Michael Meißner, Viatronix Inc., USA
Male head scan
Details
Dataset Name: vis_male
Dataset Type: uint8
Dataset Size: [128, 256, 256]
Dataset Spacing: [1.57774, 0.995861, 1.00797]
Dataset Scales: 2
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/vis_male.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/vis_male.ome.zarr
Acknowledgement: National Library of Medicine, National Institutes of Health, USA
A microCT scan of dried wood branch (hazelnut).
Details
Dataset Name: woodbranch
Dataset Type: uint16
Dataset Size: [2048, 2048, 2048]
Dataset Spacing: [1.8e-05, 1.8e-05, 1.8e-05]
Dataset Scales: 5
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/woodbranch.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/woodbranch.ome.zarr
Acknowledgement: The Computer-Assisted Paleoanthropology group and the Visualization and MultiMedia Lab at University of Zurich (UZH)
Car part reconstructed from projections.
Details
Dataset Name: zeiss
Dataset Type: uint8
Dataset Size: [680, 680, 680]
Dataset Spacing: [1, 1, 1]
Dataset Scales: 3
Dataset HTTPS URL: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2/zeiss.ome.zarr
Dataset S3 URL: s3://ome-zarr-scivis/v0.5/96x2/zeiss.ome.zarr
Acknowledgement: Steffen Frey and Daimler AG
- marschner_lobb - 6.9e+04
- nucleon - 6.9e+04
- silicium - 1.1e+05
- fuel - 2.6e+05
- neghip - 2.6e+05
- tooth - 1.6e+06
- blunt_fin - 2.1e+06
- hydrogen_atom - 2.1e+06
- shockwave - 2.1e+06
- frog - 2.9e+06
- lobster - 5.5e+06
- mri_woman - 7.1e+06
- mri_ventricles - 8.1e+06
- engine - 8.4e+06
- vis_male - 8.4e+06
- statue_leg - 1.1e+07
- boston_teapot - 1.2e+07
- aneurism - 1.7e+07
- bonsai - 1.7e+07
- foot - 1.7e+07
- skull - 1.7e+07
- tacc_turbulence - 1.7e+07
- mrt_angio - 2.4e+07
- csafe_heptane - 2.8e+07
- carp - 3.4e+07
- duct - 3.7e+07
- stent - 4.6e+07
- pancreas - 6.3e+07
- bunny - 9.5e+07
- backpack - 9.8e+07
- present - 1.1e+08
- neocortical_layer_1_axons - 1.1e+08
- prone - 1.2e+08
- christmas_tree - 1.3e+08
- magnetic_reconnection - 1.3e+08
- vertebra - 1.3e+08
- hcci_oh - 1.8e+08
- zeiss - 3.1e+08
- marmoset_neurons - 3.3e+08
- stag_beetle - 3.4e+08
- pawpawsaurus - 6.7e+08
- spathorhynchus - 7.9e+08
- kingsnake - 8.3e+08
- miranda - 1.1e+09
- chameleon - 1.1e+09
- beechnut - 1.6e+09
- jicf_q - 1.7e+09
- synthetic_truss_with_five_defects - 1.7e+09
- richtmyer_meshkov - 8.1e+09
- woodbranch - 8.6e+09
- pig_heart - 1.1e+10
- aneurism
- backpack
- beechnut
- bonsai
- boston_teapot
- bunny
- carp
- chameleon
- christmas_tree
- engine
- foot
- kingsnake
- lobster
- mrt_angio
- pancreas
- pawpawsaurus
- pig_heart
- present
- prone
- skull
- spathorhynchus
- stag_beetle
- statue_leg
- stent
- synthetic_truss_with_five_defects
- vertebra
- vis_male
- woodbranch
- zeiss
- blunt_fin
- csafe_heptane
- duct
- fuel
- hcci_oh
- hydrogen_atom
- jicf_q
- magnetic_reconnection
- marschner_lobb
- miranda
- neghip
- nucleon
- richtmyer_meshkov
- shockwave
- silicium
- tacc_turbulence
The OME-Zarr Open SciVis Datasets are freely available for download and use by the scientific visualization community.
To load a dataset in Python, use the following example code:
pip install ngff-zarr s3fs matplotlibimport ngff_zarr as nz
import zarr.storage
from rich import print
from matplotlib import pyplot as plt
store = zarr.storage.FsspecStore.from_url(
's3://ome-zarr-scivis/v0.5/64x2/engine.ome.zarr',
read_only=True,
storage_options={'anon':True}
)
multiscales = nz.from_ngff_zarr(store)
print(multiscales)Multiscales(
images=[
NgffImage(
data=dask.array<from-zarr, shape=(128, 256, 256), dtype=uint8, chunksize=(64, 64, 64), chunktype=numpy.ndarray>,
dims=['z', 'y', 'x'],
scale={'z': 1.0, 'y': 1.0, 'x': 1.0},
translation={'z': -64.0, 'y': -128.0, 'x': -128.0},
name='image',
axes_units={'z': None, 'y': None, 'x': None},
computed_callbacks=[]
),
NgffImage(
data=dask.array<from-zarr, shape=(128, 128, 128), dtype=uint8, chunksize=(64, 64, 64), chunktype=numpy.ndarray>,
dims=['z', 'y', 'x'],
scale={'z': 1.0, 'y': 2.0, 'x': 2.0},
translation={'z': -64.0, 'y': -127.5, 'x': -127.5},
name='image',
axes_units={'z': None, 'y': None, 'x': None},
computed_callbacks=[]
)
],
metadata=Metadata(
axes=[Axis(name='z', type='space', unit=None), Axis(name='y', type='space', unit=None), Axis(name='x', type='space', unit=None)],
datasets=[
Dataset(
path='scale0/engine',
coordinateTransformations=[
Scale(scale=[1.0, 1.0, 1.0], type='scale'),
Translation(translation=[-64.0, -128.0, -128.0], type='translation')
]
),
Dataset(
path='scale1/engine',
coordinateTransformations=[
Scale(scale=[1.0, 2.0, 2.0], type='scale'),
Translation(translation=[-64.0, -127.5, -127.5], type='translation')
]
)
],
coordinateTransformations=None,
omero=None,
name='image'
),
scale_factors=None,
method=None,
chunks=None"
)plt.imshow(multiscales.images[1].data[64,:,:])
plt.show()
For additional tools to read or visualize OME-Zarr datasets, see the Next Generation File Format (NGFF) tools index.
All datasets are currently available in two OME-Zarr format versions, Version 0.4 (Zarr 2-based), and Version 0.5 (Zarr 3-based).
- 0.4 : OME-Zarr Version 0.4
- 0.5 : OME-Zarr Version 0.5
Datasets are also available with different z,y,x chunk sizes.
- 64 : 64x64x64
- 96 : 96x96x96
- 128 : 128x128x28
For the OME-Zarr v0.5, datasets, datasets are also available with different sharding settings.
- 0 : 0x0x0 (no sharding)
- 2 : 2x2x2 (two chunks per shard in each dimension)
- 4 : 4x4x4
For OME-Zarr v0.4, only 0 (no sharding) is available.
The URL formats are:
- https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v{version}/{chunks}x{shards}/{dataset_name}.ome.zarr
- s3://ome-zarr-scivis/v{version}/{chunks}x{shards}/{dataset_name}.ome.zarr
The datasets in this collection are provided under various open licenses, including Creative Commons and public domain licenses. Please refer to the individual dataset descriptions for specific licensing information.
The OME-Zarr Open SciVis Datasets generation code is licensed under the Apache 2.0 License.
We would like to acknowledge the following individuals and organizations for their contributions and support:
- Pavol Klacansky for curating the original Open SciVis Datasets collection and making it freely available to the scientific visualization community.
- The Open Microscopy Environment for developing the OME-Zarr file format and promoting open, collaborative standards for bioimaging data.
- Amazon Web Services (AWS) for hosting the OME-Zarr Open SciVis Datasets on the AWS S3 platform through the AWS Open Data Program.
- NumFOCUS for supporting the development and maintenance of open-source scientific computing tools and resources.