TissueStack: an Open Source HTML5 web based imaging viewer
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1
University of Queensland, Australia
Web based viewing of large 3D datasets is now a critical part of imaging research. This has been driven by multiple efforts to make available large collections of histological, optical and electron Microscopy data. It is critical that the web applications to view and serve this data are robust, available on multiple platforms, have a scalable view of data and are intuitive to use for novel users. Existing tools that are capable of presenting tri-planar views of large datasets rely upon custom web extensions such as Adobe Flash, have restrictive dataset size limitations and as such are not tractable on mobile devices.
The TissueStack project was born from these goals and is now a mature product. The original use case was a large multi-site study with geographically distant generators of imaging data. This leads to the problem in which no one is sure where or how to access the current version of all the data without having to download TB's of data and trawl through it. This problem is not unique to the neuroimaging field and as such in TissueStack we made extensice use of techniques from the very closely related field of GIS (Graphical Information Systems – ie: online mapping).
The server and viewing application have a number of features: Image tiles can be either generated on the fly or Pre-tiling can be initiated via the interface. The tool is HTML5 based and thus runs on mobile devices (iOS, Android, etc). We have tested the TissueStack server on 3D datasets up to 12GB in size over a mobile data link with no significant increase in rendering time (See Figure). It supports embedding, direct links to dataset features, dataset colour mapping, intensity range adjustments, multiple views of datasets, overlays and load balancing across multiple servers. The current server has a plug in architecture and can load files in either MINC or NifTI format. An example server running on a virtual appliance in the Australian Research Cloud can be viewed at http://caivm1.qern.qcif.edu.au.
Tissuestack has so far been successfully used for neuroimaging, chemical engineering, electron microscopy, digital curation by museums and animal atlasing data. The main website and more information is available at www.tissuestack.org
TissueStack is an Open Source project and is available on GitHub (github.com/NIF-au/TissueStack). All code is licensed via the GPL v3.
Acknowledgements
This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.
Keywords:
digital atlasing,
HTML5,
Web service,
Neuroimaging,
image view
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Demo
Topic:
Digital atlasing
Citation:
Janke
A,
Lin
M,
Nicolini
O,
Waxenegger
H,
Ullmann
J and
Galloway
GJ
(2013). TissueStack: an Open Source HTML5 web based imaging viewer.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00120
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Received:
29 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Andrew Janke, University of Queensland, Brisbane, Australia, a.janke@gmail.com