Tuesday, 10 August 2021

Repositories for 3D image (and other) data

 Please send me corrections, updates, and additions!

Registry of Research Data Repositories

http://re3data.org/

Listing of many repositories in all subject areas.

FAIRsharing

https://fairsharing.org/

"A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." Lists lots of repositories, standards, and knowledge bases.

Zenodo

https://zenodo.org/

Hosted by CERN. "All fields of research. All types of research artifacts." Open data for open science. Up to 50GB per record, or by arrangement. My general favorite.

BioImage Archive

https://www.ebi.ac.uk/bioimage-archive

A free, publicly available online resource for biological images that are either associated with a peer-reviewed publication, or of value beyond a single experiment.

Figshare     https://figshare.com/

Choice of CC license.

Giga Data Base (GigaDB)   http://gigadb.org/

Uses CC0 (public domain) licensing.

iDigBio

https://www.idigbio.org/

The National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by NSF. Data and images for millions of biological specimens.

MorphoSource

http://morphosource.org/

Duke Univ. Especially for museum specimens.

(Boyer et al 2017)

Brain Image Library  

https://www.brainimagelibrary.org/

"... national public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets."

Morph·D·Base   https://www.morphdbase.de/

Morphological Description Data Base. Not easy to access.

MorphoBank    http://www.morphobank.org/

"Homology of phenotypes & a database of peer-reviewed morphological matrices"

Digital Fish Library (DFL)

http://www.digitalfishlibrary.org/

"...explores the morphological diversity of fishes using magnetic resonance imaging (MRI)"  Not open to external contributions

Digital Morphology (Digimorph)

http://digimorph.org/

Univ. Texas microCT library. Lots of fossils and other vertebrate samples, stacks, movies and more.

Dryad      http://datadryad.org/

Uses CC0 (public domain) licensing.

Phenome10k        http://phenome10k.org/

CT and surface scans of biological and palaeontological specimens (skulls).

Harvard Dataverse

https://dataverse.harvard.edu/

All kinds of data. Set up your own dataverse collection, up to 1TB. 

MorphoMuseuM (M3)

https://morphomuseum.com/

Mainly surface models. A peer reviewed, online journal that publishes 3D models of vertebrates, anatomy atlases, and 3D datasets. Also direct submission.

Aves 3D      http://aves3d.org/

Bird bones and skeletons

heidICON

https://heidicon.ub.uni-heidelberg.de/search

Image and multimedia database. Die Heidelberger Bilddatenbank, is the "Virtual Slide Collection" in progress of Heidelberg University.

Sammlungen Göttingen

https://sammlungen.uni-goettingen.de/  

Wissenschaftliche Sammlungen der Georg-August-Universität Göttingen.

Image Data Resource (IDR)

https://idr.openmicroscopy.org/about/

A public repository of reference image datasets from published scientific studies. (Williams et al 2017)

Phaidra (UniVie)

https://phaidra.univie.ac.at/

Phaidra is the repository for the permanent secure storage of digital assets at the University of Vienna.

GitHub       https://github.com/

The place for open software

New Mexico Decedent Image Database (NMDID)
https://nmdid.unm.edu/welcome  

provides researchers with access to whole human body computed tomography (CT) scans and a rich body of associated metadata.

FaceBase
https://www.facebase.org/  

Comprehensive craniofacial data (including 3D imaging datasets) from model organisms (mouse and zebrafish) and humans.

MorphoBrowser
http://morphobrowser.biocenter.helsinki.fi/  

‘MorphoBrowser’ database and interface is a 3D visualisation and searching tool for mammalian teeth, accessible over the web.

Phenome10K
http://phenome10k.org/  

A free online repository for 3-D scans of biological and palaeontological specimens.

Genetics of craniofacial shape in Mus
https://osf.io/w4wvg/  

High-resolution 3D microCT head scans of a mouse panel between C57BL/6J and A/J mouse strains and associated genotype data. Contains mCT scans of ~500 mice heads and associated cranial landmarks.

Digital Morphology Museum of Kyoto University (KUPRI)
http://dmm4.pri.kyoto-u.ac.jp/dmm/WebGallery/index.html  

DMM provides a large collection of CT and MRI tomography scans of various primates.

The Open Research Scan Archive
https://www.penn.museum/sites/orsa/Overview.html  

(formerly Penn Cranial CT Database) contains high resolution (sub-millimeter) scans of human and non-human crania from the Penn University Museum and other institutions.

GB3D
http://www.3d-fossils.ac.uk/search.cfm  

Fossils Online project, aims to develop a single database of the type specimens, held in British collections, of macrofossil species and subspecies found in the UK, including links to photographs and a selection of 3D digital models.

 

Other sources for 3D images:

The Visible Human Project

https://www.nlm.nih.gov/research/visible/visible_human.html

Full-body images of a male and female adult

Thingiverse

https://www.thingiverse.com/

Loads of cool 3D models for 3D printing

Phaidra (UniVie)

https://phaidra.univie.ac.at/

Phaidra is the repository for the permanent secure storage of digital assets at the University of Vienna.

 

A lot of these repositories and many others for various kinds of data and documents are listed at PUBLISSO (itself a repository): 
https://www.publisso.de/en/research-data-management/publishing/publisso-repository-finder/

Also good to know is DataCitehttps://datacite.org/ 


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