OME-Zarr Open SciVis Datasets

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.

Table of Contents

• Introduction
  • OME-Zarr
  • Open SciVis Datasets
  • Project Overview
• Datasets
  • Sorted by number of voxels
  • CT Scans
  • MRI Scans
  • Microscopy Datasets
  • Simulation Datasets
• Usage
• License
• Acknowledgements

Introduction

OME-Zarr

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.

Open SciVis Datasets

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.

Project Overview

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:

1. The datasets are restructured into a chunked, multi-scale form, allowing for efficient access to different resolutions and subsets of the data.

2. 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.

3. 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:

• It promotes reproducibility in research by providing standardized, easily accessible datasets that can be used as benchmarks or test cases across different studies.

• 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.

• 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.

Datasets

aneurism

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/aneurism.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/aneurism.ome.zarr)** **Acknowledgement:** volvis.org and Philips Research, Hamburg, Germany

backpack

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/backpack.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/backpack.ome.zarr)** **Acknowledgement:** volvis.org and Kevin Kreeger, Viatronix Inc., USA

beechnut

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/beechnut.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/beechnut.ome.zarr)** **Acknowledgement:** The Computer-Assisted Paleoanthropology group and the Visualization and MultiMedia Lab at University of Zurich (UZH)

blunt_fin

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/blunt_fin.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/blunt_fin.ome.zarr)** **Acknowledgement:** NASA Advanced Supercomputing Division, USA

bonsai

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/bonsai.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/bonsai.ome.zarr)** **Acknowledgement:** volvis.org and S. Roettger, VIS, University of Stuttgart

boston_teapot

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/boston_teapot.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/boston_teapot.ome.zarr)** **Acknowledgement:** volvis.org and Terarecon Inc, MERL, Brigham and Women's Hospital

bunny

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/bunny.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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.

carp

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/carp.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/carp.ome.zarr)** **Acknowledgement:** Michael Scheuring, Computer Graphics Group, University of Erlangen, Germany

chameleon

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/chameleon.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/chameleon.ome.zarr)** **Acknowledgement:** Chamaeleo calyptratus. Digital Morphology, 2003.

christmas_tree

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/christmas_tree.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/christmas_tree.ome.zarr)** **Acknowledgement:** Armin Kanitsar, 2002

csafe_heptane

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/csafe_heptane.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/csafe_heptane.ome.zarr)** **Acknowledgement:** The University of Utah Center for the Simulation of Accidental Fires and Explosions.

duct

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/duct.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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).

engine

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/engine.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/engine.ome.zarr)** **Acknowledgement:** volvis.org and General Electric

foot

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/foot.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/foot.ome.zarr)** **Acknowledgement:** volvis.org and Philips Research, Hamburg, Germany

frog

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/frog.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/frog.ome.zarr)** **Acknowledgement:** Lawrence Berkeley Laboratory, USA

fuel

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/fuel.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/fuel.ome.zarr)** **Acknowledgement:** volvis.org and SFB 382 of the German Research Council (DFG)

hcci_oh

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/hcci_oh.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/hcci_oh.ome.zarr)** **Acknowledgement:** Gaurav Bansal, Ajith Mascarenhas, and Jacqueline H. Chen.

hydrogen_atom

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/hydrogen_atom.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/hydrogen_atom.ome.zarr)** **Acknowledgement:** volvis.org and SFB 382 of the German Research Council (DFG)

jicf_q

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/jicf_q.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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).

kingsnake

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/kingsnake.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/kingsnake.ome.zarr)** **Acknowledgement:** DigiMorph.org, The University of Texas High-Resolution X-ray CT Facility (UTCT), and NSF grant IIS-9874781

lobster

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/lobster.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/lobster.ome.zarr)** **Acknowledgement:** volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA

magnetic_reconnection

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/magnetic_reconnection.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/magnetic_reconnection.ome.zarr)** **Acknowledgement:** Bill Daughton (LANL) and Berk Geveci (KitWare). Please acknowledge paper http://arxiv.org/abs/1405.4040.

marmoset_neurons

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/marmoset_neurons.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/marmoset_neurons.ome.zarr)** **Acknowledgement:** Frederick Federer, Moran Eye Institute, University of Utah

marschner_lobb

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/marschner_lobb.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/marschner_lobb.ome.zarr)** **Acknowledgement:** volvis.org and Marschner and Lobb

miranda

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/miranda.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/miranda.ome.zarr)** **Acknowledgement:** Andrew W. Cook, William Cabot, and Paul L. Miller

mri_ventricles

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/mri_ventricles.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/mri_ventricles.ome.zarr)** **Acknowledgement:** volvis.org and Dirk Bartz, VCM, University of Tübingen, Germany

mri_woman

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/mri_woman.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/mri_woman.ome.zarr)** **Acknowledgement:** Siemens Medical Systems, Inc., Iselin, NJ., USA

mrt_angio

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/mrt_angio.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/mrt_angio.ome.zarr)** **Acknowledgement:** volvis.org and Özlem Gürvit, Institute for Neuroradiology, Frankfurt, Germany

neghip

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/neghip.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/neghip.ome.zarr)** **Acknowledgement:** volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA

neocorticallayer1_axons

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/neocortical_layer_1_axons.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/neocortical_layer_1_axons.ome.zarr)** **Acknowledgement:** V De Paola, MRC Clinical Sciences Center, Imperial College London

nucleon

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/nucleon.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/nucleon.ome.zarr)** **Acknowledgement:** volvis.org and SFB 382 of the German Research Council (DFG)

pancreas

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/pancreas.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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.

pawpawsaurus

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/pawpawsaurus.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/pawpawsaurus.ome.zarr)** **Acknowledgement:** Matthew Colbert, 4 February 2014

pig_heart

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/pig_heart.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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.

present

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/present.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/present.ome.zarr)** **Acknowledgement:** Christoph Heinzl, 2006

prone

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/prone.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/prone.ome.zarr)** **Acknowledgement:** volvis.org and Walter Reed Army Medical Center, USA

richtmyer_meshkov

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/richtmyer_meshkov.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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

shockwave

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/shockwave.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/shockwave.ome.zarr)** **Acknowledgement:** volvis.org

silicium

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/silicium.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/silicium.ome.zarr)** **Acknowledgement:** volvis.org and VolVis distribution of SUNY Stony Brook, NY, USA

skull

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/skull.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/skull.ome.zarr)** **Acknowledgement:** volvis.org and Siemens Medical Solutions, Forchheim, Germany

spathorhynchus

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/spathorhynchus.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/spathorhynchus.ome.zarr)** **Acknowledgement:** Matthew Colbert, 17 February 2005

stag_beetle

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/stag_beetle.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/stag_beetle.ome.zarr)** **Acknowledgement:** Meister Eduard Gröller, Georg Glaeser, Johannes Kastner, 2005

statue_leg

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/statue_leg.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/statue_leg.ome.zarr)** **Acknowledgement:** volvis.org and German Federal Institute for Material Research and Testing (BAM), Berlin, Germany

stent

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/stent.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/stent.ome.zarr)** **Acknowledgement:** volvis.org and Michael Meißner, Viatronix Inc., USA

synthetictrusswithfivedefects

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/synthetic_truss_with_five_defects.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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.

tacc_turbulence

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/tacc_turbulence.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/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.

tooth

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/tooth.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/tooth.ome.zarr)** **Acknowledgement:**

vertebra

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/vertebra.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/vertebra.ome.zarr)** **Acknowledgement:** volvis.org and Michael Meißner, Viatronix Inc., USA

vis_male

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/vis_male.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/vis_male.ome.zarr)** **Acknowledgement:** National Library of Medicine, National Institutes of Health, USA

woodbranch

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/woodbranch.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/woodbranch.ome.zarr)** **Acknowledgement:** The Computer-Assisted Paleoanthropology group and the Visualization and MultiMedia Lab at University of Zurich (UZH)

zeiss

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 **[Interactive visualization](https://kitware.github.io/itk-vtk-viewer/app/?image=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/zeiss.ome.zarr)** **[Interactive structure](https://ome.github.io/ome-ngff-validator/?source=https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x0/zeiss.ome.zarr)** **Acknowledgement:** Steffen Frey and Daimler AG

Sorted by number of voxels

1. marschner_lobb - 6.9e+04
2. nucleon - 6.9e+04
3. silicium - 1.1e+05
4. fuel - 2.6e+05
5. neghip - 2.6e+05
6. tooth - 1.6e+06
7. blunt_fin - 2.1e+06
8. hydrogen_atom - 2.1e+06
9. shockwave - 2.1e+06
10. frog - 2.9e+06
11. lobster - 5.5e+06
12. mri_woman - 7.1e+06
13. mri_ventricles - 8.1e+06
14. engine - 8.4e+06
15. vis_male - 8.4e+06
16. statue_leg - 1.1e+07
17. boston_teapot - 1.2e+07
18. aneurism - 1.7e+07
19. bonsai - 1.7e+07
20. foot - 1.7e+07
21. skull - 1.7e+07
22. tacc_turbulence - 1.7e+07
23. mrt_angio - 2.4e+07
24. csafe_heptane - 2.8e+07
25. carp - 3.4e+07
26. duct - 3.7e+07
27. stent - 4.6e+07
28. pancreas - 6.3e+07
29. bunny - 9.5e+07
30. backpack - 9.8e+07
31. present - 1.1e+08
32. neocorticallayer1_axons - 1.1e+08
33. prone - 1.2e+08
34. christmas_tree - 1.3e+08
35. magnetic_reconnection - 1.3e+08
36. vertebra - 1.3e+08
37. hcci_oh - 1.8e+08
38. zeiss - 3.1e+08
39. marmoset_neurons - 3.3e+08
40. stag_beetle - 3.4e+08
41. pawpawsaurus - 6.7e+08
42. spathorhynchus - 7.9e+08
43. kingsnake - 8.3e+08
44. miranda - 1.1e+09
45. chameleon - 1.1e+09
46. beechnut - 1.6e+09
47. jicf_q - 1.7e+09
48. synthetictrusswithfivedefects - 1.7e+09
49. richtmyer_meshkov - 8.1e+09
50. woodbranch - 8.6e+09
51. pig_heart - 1.1e+10

CT Scans

• 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
• synthetictrusswithfivedefects
• vertebra
• vis_male
• woodbranch
• zeiss

MRI Scans

• frog
• mri_ventricles
• mri_woman

Microscopy Datasets

• marmoset_neurons
• neocorticallayer1_axons

Simulation Datasets

• 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

Usage

The OME-Zarr Open SciVis Datasets are freely available for download and use by the scientific visualization community.

Python Loading Example

To load a dataset in Python, use the following example code:

shell pip install ngff-zarr s3fs matplotlib

```python import ngff_zarr as nz import zarr.storage from rich import print from matplotlib import pyplot as plt

store = zarr.storage.FsspecStore.fromurl( 's3://ome-zarr-scivis/v0.5/64x2/engine.ome.zarr', readonly=True, storageoptions={'anon':True} ) multiscales = nz.fromngff_zarr(store)

print(multiscales)

```

python 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" )

python plt.imshow(multiscales.images[1].data[64,:,:]) plt.show()

---

Additional tools

For additional tools to read or visualize OME-Zarr datasets, see the Next Generation File Format (NGFF) tools index.

Dataset Formats

version

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

chunks

Datasets are also available with different z,y,x chunk sizes.

• 64 : 64x64x64
• 96 : 96x96x96
• 128 : 128x128x28

shards

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.

URL format

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

License

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.

Acknowledgements

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.