Announcing TissueStack

TissueStack was originally designed for use in the 3D medical and scientific imaging field for data from 3D micro-CT, MRI and restacked histology data. The viewer has since been used for multiple datasets including museum specimens, coal mining samples and Electron Microscopy data.

The original motivation for TissueStack came from the burgeoning size of micro-MRI and micro-CT datasets in scientific experiments. For a typical mouse brain imaging study this can amount to 12-15GB for a single scan. This problem is only exacerbated when re-stacked optical imaging (Histology) data is added to the analysis as these datasets can be up to 1TB in size. This presents a large barrier to collaborative research as it is difficult to share data between sites and keep collaborators up to date with the latest observations. What was needed was a 3D dataset viewing system that could be viewed remotely and had the ability to federate and overlay datasets from multiple sites, from these set of requirements TissueStack was born.

So far, TissueStack has been used by researchers from UQ (Brisbane) and Curtin (Perth) to collaboratively annotate the highest resolution model of mouse anatomy to date as part of the AMBMC project. Without the abilities of TissueStack to link to specific parts of the data, efforts to identify sub-structures were reduced to lengthy conference calls in which the collaborators attempted to sync their views of the same data.

From a technical standpoint, TissueStack is a web based HTML5 3D dataset viewer that generates image tiles on the fly, the main interface is shown below.

The main TissueStack interface view
The viewer has been designed to mimic web based map viewing sites such that users can easily navigate. A demonstration of TissueStack can be seen here: http://caivm1.qern.qcif.edu.au/ There is also a mobile/tablet version of TissueStack with all the same functionality as the "desktop" version. The appropriate version of the site is loaded based upon the viewers current viewing platform.

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