Embedded Files
The data types below are examples from which testing and tutorials can draw. Please add more data types and examples as you find them. And try finding software that will let you open and visualize the data, whether in VR or otherwise. Then document it, at least in your journal.
For an abbreviated list of common data types, a brief definition of each type, and recommended/feasible software to use with each type, please see the Software Recommendations by Data Type page.
Please note: many of the following files are very large (we're talking up to around a hundred MB for some of these)! Additionally, this page is a continual work in progress. The categories of data are not exhaustive and are listed in no partincular order, so be prepared for the page to be somewhat messy.
Scalar Volume Data
Scalar Volume Data
Description: 3D array of data values where each point corresponds to a single value
Data with Collaborators:
Connectome Volume Data from Thomas Serre
Rat Heart Vessels from Kareen Coulombe
micro-CT data - test.vtk
Edith Mathiowitz's electron microscopy volume data [likely to be available soon]
Live biological cells from Mohak Patel and Ian Wong
Data without Collaborators:
Iron Binding Protein Model
This file is also included as a sample data file in the vtk download
Pig Chewing Model
2D Image Data
2D Image Data
Description: 2D array of data values that can be reduced to an RGB image before viewing or interactively during viewing.
Data without Collaborators
Colored Mars Images
Simple Animals (from Felice Frankel at MIT)
Cell Image Library - 2D images of many different types of cells
Electron Microscopy Public Image Archive (EMPIAR)
Lots of 2D microscopy data
2D Vector Field or Flow Data
2D Vector Field or Flow Data
Description: A magnitude and direction at each point in a plane. Sometimes such vector fields can represent 2D fluid flow, but they can be other things, as well. Can be time-varying.
3D Vector Field or Flow Data
3D Vector Field or Flow Data
Description: A magnitude and direction at each more in 3D space. Can be 3D flow. Can be time-varying.
Data with Collaborators
Narragansett Bay/Rhode Island Sound Circulation Model - Bruce Campbell and Kevin Rosa
http://blackfish.cs.brown.edu/PODS/csci/fgs220TS_his.nc (12.57 GB) - sample data in NetCDF4 format for run 220 of circulation model
http://blackfish.cs.brown.edu/PODS/csci/data_directory.png (600 KB) - screen capture of data directory for fgs220TS_his.nc
http://blackfish.cs.brown.edu/PODS/csci/Example_reader.ipynb (10 KB) - Python notebook example for using fgs220TS_his.nc
http://blackfish.cs.brown.edu/PODS/csci/drifters110.zip (8.2 MB) - Example x, y, z coordinates for subsample of virtual drifters for run 110 (indexed by drifter #)
Vibrating Cylinder Flow - George Karniadakis and Zhicheng Wang
Contains 10 .plt files each of which contains 12 components of data:
(x, y, z) position coordinates
(u, v, w) velocity components in the x, y, z directions
p is pressure
vorticity_x, vorticity_y, vorticity_z
Q, second invariant of the velocity gradient
Data without Collaborators
Pipette Simulation Data
Building Downwash Simulations
Turbulence Decay
Point Cloud Data
Point Cloud Data
Description: data that represents a collection of points in 2D or 3D space.
File Types:
las files: Lidar data comes comes in many forms, however, las files are one of the most popular Lidar data formats. An las file is a binary file which contains point cloud data, stored as X, Y, Z coordinates, and a header which contains file metadata, RGB information, GIS information, and many other optional fields. For more detailed information on las files, see the official las specification.
Data with Collaborators:
Ecology data from EEB Professor Jim Kellner and postdoc Loren Albert:
Data without Collaborators:
Sample NEONDS Sample LiDAR Point Cloud Data:
Sample Velodyne .pcap files:
City of Montreal, Canada LiDAR
http://donnees.ville.montreal.qc.ca/dataset/lidar-aerien-2015 (note that this page is written in French)
Point Cloud Visualization Software:
Point Cloud Processing Software:
Comparisons:
Tutorials:
Tutorial on Python-PCL
Tutorial on Converting .las files to .out files: Laspy Tutorial
Tutorial on Lidar Paraview to Blender
Tutorial on viewing .pcap files in Veloview.
Papers:
Summaries of papers on processing and rendering LiDAR data.
Created by Ross Briden and Ronald Baker; (T) signifies whether a particular software package has been tested; ($) signifies license required.
Data Cube
Data Cube
see https://en.wikipedia.org/wiki/Data_cube
Data without Collaborators
Fidelity Financial Data
Planetary Geology Imaging Data
Planetary Geology Imaging Data
Description: This might be an amalgam of different data types, including collections of stars, collections of galaxies, outward-looking imagery (as from a telescope), or inward looking imagery (as from a satellite of a planet). Some such data is 2D imaging data, but with a particular underlying space, e.g., Earth, the moon, or Mars.
Data without Collaborators
NASA Global Imagery Browser Services (GIBS):
GIBS is a database of satellite imagery data collected by NASA JPL; the database supports an extensive REST API, however, it can be somewhat complicated to use.
GIBS returns satellite data in the form of tiles or maps (in Mercator projection)
Earthdata is a massive database of atmospheric, land, and ocean data operated by NASA
OpenSpace data -- OpenSpace software is listed below as a way to look at many different kinds of data from NASA missions. But it has been somewhat challenging to get to work in the YURT, so it might be worth exploring other software tools for visualizign and interacting with those types of data.
Software:
OpenSpace software views some kinds of data of these types, and it has the potential to generalize to more. It almost runs in the Yurt and does run on desktops and HMD's.
CLARITY Imaging Data
CLARITY Imaging Data
Description: CLARITY imaging is a relatively new brain imaging technique which utilizes chemical compounds to visualize brain anatomy with vivid accuracy. CLARITY imaging data is typically represented as a stack of 2D images, which means that CLARITY data can be easily processed by Paraview and other software!
Data without Collaborators:
Software:
Paraview (T)
Matlab - in particular, Matlab has built-in libraries to visualize volume data, such as CLARITY imaging data.
Tutorials:
Visualizing CLARITY imaging data in Paraview.
Papers:
A technical description of CLARITY imaging.
Stanford provides a database of journal articles which utilize CLARITY imaging.
Similar to:
MRI Brain Imaging
CT Brain imaging
Created by Ross Briden; (T) signifies whether a particular software package has been tested.
MRI Imaging Data
MRI Imaging Data
Description: MRI imaging data comes in many forms, often depending on the type of MRI machine utilized when scanning a patient. Two of the most common MRI data formats are NIfTi and DICOM. Luckily, most MRI processing software can easily convert between these two formats, so we will focus on visualizing and processing only NIfTi files. For an in-depth comparison between NIfTi and DICOM, see Medical Imaging Formats.
Data:
Brain Tumor Segmentation Challenge (BRATS) - BRATS is a comprehensive MRI brain tumor data set comprised of 243 MRI scans, expertly labeled based on tumor pathology.
Alzheimer's Disease Neuroimaging Initiative (ADNI) - ADNI contains a collection of over 3000 MRI scans of Alzheimer's patients, captured over several years and with varying MRI scanners.
VR Brain Tumor Surgery - Robert Gilbert ***insert data
Note that both the BRATS and ADNI data sets are not public and must be requested.
Software:
Papers:
Human brain functional MRI and DTI visualization with virtual reality: an in-depth overview of VR visualization of MRI data.
The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS): an overview of the BRATS data set.
Medical Imaging Formats: a comprehensive comparison of the most popular MRI data formats.
Similar to:
CLARITY Brain Imaging
CT Brain imaging
Created by Ross Briden; (T) signifies whether a particular software package has been tested.
Network Data
Network Data
Data without Collaborators
Twitter API
Probably the easiest social media API to use; clearly defined data types and properties (just Tweets associated with users and their info)
Access Tweets in realtime; filter by many different properties
Access previous Tweets for other types of analysis
Apply for Twitter Developer tools here
2012 US election tweets - Microsoft Research
Daily geolocated tweets - Microsoft Research
Citation network dataset
Contains citation data extracted from Microsoft Academic Graph and other academic databases
DIMACS Shortest Path Challenge - Center for Discrete Mathematics and Theoretical Computer science
http://users.diag.uniroma1.it/challenge9/data/USA-road-d/USA-road-d.USA.gr.gz
Graph data that models distances between many major U.S. towns and cities (23,947,347 nodes)
US Flight Data (1990 - 2009)
Polygonal Model Data
Polygonal Model Data
Description: 3D data stored as polygonal meshes
Found in many 3D file extensions that hold 3d data points: OBJ, DAE, FBX, etc
Programs that use and view polygonal model data that could be YURT usable:
Unity, Blender, Unreal, Paraview
Unlikely to be YURT usable:
Maya, Adobe Dimension
Data without Collaborators
YURT Supernova (from Elaine Jiang)
The .vtk files (find them in the github above) listed below are all data sets used by the Supernova program, which models the Cas A supernova
Neutron Star
cco-ascii.vtk
Fiducial Jets
newjets-ascii.vtk
FeK (Chandra Telescope)
fekcorr-ascii.vtk
ArII (Spitzer Telescope)
newar-ascii.vtk
Si (Chandra Telescope, HETG)
newhetg-ascii.vtk
Outer Knots
newopt-ascii.vtk
Reverse Shock Sphere
newsi-ascii.vtk
World Vector Shorelines
http://www.earthmodels.org/data-and-tools/coastlines/World_Vector_Shorelines.vtp
Surface model of the world's shorelines
City of Adelaide 3D Model
Open City Model
Time Series Data
Time Series Data
Description: Series of data points indexed by time.
Data with Collaborators
CIT time series data
Data without Collaborators
Genomics Data
Genomics Data
Description: Data that captures various genetic information such as variances in genome sequences, DNA sequences, and other genetics information
Data without Collaborators
Genome variant calls of chromosome 22 - Microsoft Research
RGB-D
RGB-D
Description: Output from cameras with proximity sensors contain an extra channel for depth. Its value ranges from 0-255 just like color. It is often visualized alone as grayscale.
Example
https://sumochallenge.org has output from a 360º scan around a room
MIDI Data
MIDI Data
Description: MIDI (Musical Instrument Digital Interface) data allows musical instruments and other hardware to communicate with each other. MIDI holds information on notes and how they are played (for example note on, velocity, modulation, note duration, note off, etc.). In this form, MIDI attemps to digitally communicate the features of a musical performance.
MIDI visualization in Unity - Packages, Assets, and Helpful Libraries:
Maestro MIDI Player Tool Kit: Asset tool to play MIDI files in your Unity application
Unity Asset (pro version) - able to read from MIDI input devices
Minis: Package that adds MIDI input device support to Unity's new Input System
NAudio: Open-source C# .NET audio library
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