Pixel Values: Lookup Files

The development branch of TissueStack now contains code to allow a text/label look-up by grayscale value/RGB triple defined in a file of the following layout:

0 0 0 0 Black (Background)
1 197 197 99 yellow (hot)
2 170 170 0 middle of brain (spectral)
3 167 167 0 Center
  • The number of required columns has to be 5 where the leading one is an at the moment unused number increment and the last column contains the associated text/label
  • The separator has to be tabs!
  • For gray-scale look-ups just set column 2 - 4 (RGB) to the desired gray-scale value


Version 0.9 (GPL3)

TissueStacks' version 0.9 source code is now available under the GNU General Public License (Version 3).


The main feature of this version is the overlay of 2 data sets in the desktop version of the software:

To enable overlay viewing, simply go into the ADMIN tab and select the appropriate option, then select the two data sets to compare.

  • If only option "Synchronize Data Sets" is checked, both data sets are displayed, the first on top, the second beneath. When navigating within either one of the two, the other will "follow"
  • The "natural" order of the overlay is such that, out of 2 selected data sets, the one that comes first in the tree view will be below, the second on top.

Additionally, the transparency wheel enables the user to control the transparency of the top data set, the swap icon exchanges the order of the overlay:

Besides the overlay feature, TissueStack now reads the color maps (more flexibly) from a directory, provided they follow a simple 4 column structure, separated by a space e.g:
0.0  0.0  0.0  0.0
1.0  0.0  1.0  0.0


Functionality Update

Task Management

As promised in the previous blog post Tissue Stack can now do image format conversions and pre-tiling more conveniently through the user interface:

Any of the given options above operate on source files in the upload directory only.
As mentioned before the formats supported are Nifti and Minc 2.

It's worth noting that Nifti and Minc 2 inputs have to be converted to our internal "raw" format prior to adding them to the local instance's configuration (as displayed in the "Data" tab tree on the left panel), otherwise you'll get a corresponding pop-up that tells you exactly that ;-)

Data Set Value Display

So far only the coordinates were displayed for the point that marks the cross-hair position. Now there is an additional field in the UI that gives you the underlying value as a single figure or an rgb triple in case you have a color map applied:

If the uploaded file had an original value range that was different from the 256 gray scale values, the canvas pixel value will get mapped back to that original range so that the original value can be displayed.

Upcoming Features:

1) Display of look-up values for Data Set pixels: Given a look-up table, the text field that for now only displays the underlying pixel's value will also give you the string associated in the look-up table.

2) Import and display of RGB data sets

3) ANDS data set registration: Optionally, if you add a data set to the configuration, meta-information will be stored in an xml which can then be harvested by ANDS => http://ands.org.au/