Histology registration

Hey, as a part of our Masters’ project, we are trying to register a stack of histological slices and then we can easily see them with “Image->Stacks->Orthogonal views” or “Plugins->Volume viewer” for example. But what we also would like to do is reconstruct a 3D surface viewable in “Plugins->3D viewer”. After registration, many of the slices have black background because of registering. How do we go about this problem to make only the blue parts stand out in the image and ALL the rest leave BLACK? Or in other words, leave out the background so that we get a 3D model? Any help will be highly appreciated, thanks!

I would try segmentation of the slices so you can remove the background and select your Region of Interest(s). For my work, I segment in Amira which is a costly software; however, segmentation in ImageJ and other freeware is also possible. In my experience, segmentation leads to better quality reconstructions and would definitely fix your problem. You can check this link out, but whatever software you choose for segmentation, the concepts stay the same. Best of Luck!


given that the different structures have distinct colors, I guess there lies a possible solution to the problem. You can select a structure using color thresholding.
If you don’t want to script this, then the would be something like:

  • Image > Adjust > ColorThresholder
  • there hit the select button
  • Analyze > Tools > ROI Manager
  • there hit the add button
  • finally you can paint you selection using the “fill” functionality (button on the ROI Manager UI: More > Fill)

hope that helps