FNXCT : Software to analyse fibre networks of paper in XCT images

Developed by Erik Wernersson

Features

• Visualisation and navigation throught XCT images of paper materials
• Manual selection of fibres
• Automated analysis based on manually selected fibres

Screenshots

Screenshots from version 2013-03-18.

Code

As it is:

• code20150513.zip

Data

One volume is available for download to show how the pre processing is supposed to be done. The data is property of Innventia.

• testVolume.mat (134 MB)

Documentation

Installation

• This is not tested with the latest matlab versions, i.e, R2014b and above. Changes to the graphics systems might cause problems.
• Download and extract the latest version under code above.
• Compile C++ code by running compileCPPfiles.m, this requires that you have a compiler installed. We have used GCC (https://gcc.gnu.org/)
• Prepare a volume (see below)
• start main.m
• If you get an error message that 'first' does not exist, just set it to something, i.e., first=10 in MATLAB.

Volume preparation

1. Create a 3D matrix of type uint8 called V, e.g.:
V = zeros([size(I,1), size(I,2), numberOfImages], 'uint8');
2. Prepare the data so that 0 corresponds to air and that 255 corresponds to fibre so that 128 corresponds to half fibre and half air.
3. Copy the data to V
4. Save V in a .mat file, i.e.,
save('-v7.3','myvolume.mat', 'V')
5. Run main.m and select myvolume.mat

Usage

At the moment, there is no documentation other than this site, the paper and the code. The program is intended to be used in the following manner:

• Run main and select a volume that you have prepared in the file dialogue (start with the dest data set given above).
• For each fibre, use the first three buttons from top to bottom to select the fibre.
  • Press the 'XY' button, this will show a sum projection of a region in the image.
  • Select the window and resize it as you wish. Then press '2' to go into slide mode. Press down the left mouse button and drag up and down to scroll in the image. When you are at a good spot, release the mouse button.
  • Press '1' to go into selection mode. Left click on the image and a yellow marker will appear. Add a few of these to delineate a fibre. The markers can be moved around by clicking and dragging them. They can be removed by clicking them with the right mouse button.
  • You might need to switch between selection mode and scroll mode a few times to select fibres that are not completely planar.
  • When satisfied, press the ZT button in the menu. That will bring up two new windows for delineating in the perpendicular view. At this point, don't edit the markers in the XY view.
  • Edit the markers in the TZ view in the same was as in the XY view. Use the blue slider to see how the cross sections look (cross view window).
  • When satisfied, press the third button in the menu, 'save'. And repeat the steps above for another fibre.
• When you don't want to select more fibres, you can look at them using the 'show3d' button, and calculate some properties with the 'statistics' button. Note that some parameters need to be tuned for each sample to adjust for the fibre morphology.