Seeking plugin to retain 3D stack, allow clicking through 2D images

Hi all,

Apologies in advance if this is well-covered terrain, but I haven’t been able to find it anywhere (and it’s clumsy to search for). Basically I’m trying to speed up my workflow, and I’m wondering if a plugin exists that I’m unaware of that would help.

I do lots of image stacking, registration, and 3D modeling. My dataset currently has over 150 samples that I’m working with, most with 100+ individual images. I have the registered images saved in folders, and generally use 3DViewer. Right now, for any given sample I want to look at, I have to

(1) Load the image sequence, (2) Set the scale (doing this manually from a separate image of the scale, since I don’t want the scale bar in my 3D model), (3) Set the slice depth (voxel depth), (4) Invert the images, (5) Run 3D Viewer. I know this doesn’t take that long, but over the number of samples I work on, this workflow slows me down considerably.

Things that would help me tremendously, if they exist.

  1. A way to save the scale and voxel depth settings (maybe in the containing folder, so they just load up automatically when I open the folder).
    2 [most important]. A way to have the 3d model appear automatically when I load a folder, and to be able to click through on individual slices and have the corresponding 2D image from that level of the 3D model appear alongside the 3D model. I’m thinking (left screen, 3D model from the side), (right screen, 2D image that changes as I click around the 3D model).
  2. Is there a way for 3D Viewer to model in such a way that treats white space as empty, rather than just black space? My images all have white backgrounds, but loading this in 3D viewer gives me a solid white block. Thus, I have to invert my image sequence, get a black background just in order to see the sample.

Thanks in advance!

1 Like

Have you tried writing a macro to automatize at least part of the process?

If your white background has always the same value, you can try to replace it by black before calling the 3D viewer. There is a replace value plugin in MorphoLibJ and also by default in Fiji (under Plugins > Process).