Version 0.7

Version 0.7 holds quite a few new features and contains some important bug-fixes to make the TissueStack ImageServer  component more stable:

  • Image Service (Direct Querying & Tiling on the fly) - Image Format Optimization 

The Image Server can now convert MINC files to our "own" RAW file format which is very rudimentary with just a header but data redundancy for 3D volumes so that data for each dimension can be read sequentially (lseek() with offset) and therefore access is both much easier and faster.
As a thumb of rule, the size of the raw file is bigger than the original file although the increase is not as dramatic as perhaps expected since space is saved by storing the information as unsigned bytes, a bit depth more than sufficient for image visualization.

Moreover, the format leaves room for further speed optimization by memory mapping, something that may come further down the track.

In summary, direct querying of even larger files is now absolutely possible whereas before the absolute upper limit was 1 GB. It is however highly recommended that even smaller MINC files be converted to our RAW format as the performance improvement is vast.

  • Image Service (Direct Querying & Tiling on the fly) - Color Mapping
The color maps (hot, spectral) existed already for pre-tiled data sets. This was accomplished on the client side by the canvas element. Now direct querying of data sets includes the same functionality on the server side.

  • Front End Web Page - Admin Section - File Uploads and Dataset Imports

The front-end has now its own "admin section" which is secured by an admin password for the time being. It enables people to upload their MINC files and then import them into the configuration database which adds the data set to the tree list for selection and viewing:

  • Front End Web Page - Scale Bar
The main view canvas of the data set incorporates a scale bar which tells you about the unit and resolution of the screen data. The information is extracted from the original MINC file and written to the database as well as to the RAW file in case of a conversion.

  • Front End Web Page - Opening of a data set via a copy-able link

As illustrated in the screen-shot above, there is now an easy way of copy and pasting a link to the data set viewed into the browser address bar. The parameters that can  be used are:

ds: data set id (as also shown in the navigation tree)
plane: the plane (e.g.: x,y,z)
x,y and z for the coordinates (in real world coordinates)
zoom: the zoom level.

This functionality is also available for the embedded version of Tissue Stack but it has to be done programmatically in js, like this for instance:

var initOpts = {
plane: 'y',
zoom : 6,
x: 50,
y: -43,
z: 80

Work in Progress: 

  1. Conversion of Nifti files to RAW files
  2. Contrast Slider and contrast range manipulation of server side