ImageJ, Extended Depth of Field and 3D Viewer

Good day!

  1. I have a problem with EDF 3D plugin when I want to display a 3D image of stack. I do the next steps: file -> import -> image sequence // plugins -> extended depth of field -> 3D EDF -> run // I am waiting and get processed images as

    and Texture

    After, I want to display 3D image and click ‘display’. So, I get error

  2. Also, I have a problem with 3D Viewer. Why I do not get normal volume image?

Thank you!

***I attached images for more details
New (5.9 MB)

Hello and welcome @zekan96,
I’m not familiar with the EDF plugin, but for viewing topographic images you should use the Interactive 3D surface plot, not 3D viewer. You can also apply a texture. It comes bundled with Fiji as far as I remember.
Hint: avoid JPG images for scientific work because it’s lossy compression.


Thank you, Nicolas! I try to do your advice!

@Nicolas, good day! It very helped me!

However, how can I scale/change z-axis considering real height difference? Or how can I set the lower and upper range of real z-position given from an optical microscope for image stacking or 3D visualization?

Hi @zekan96,

If the EDF plugin doesn’t let you the opportunity to set the height scale, the values in your final 32-bit image should be comprised between 0 and the number of individual images (minus 1). Is that the case?
If so, you can multiply the 32-bit image (Process/Math/Multiply) by the spacing between the images. Then the final image should be correctly calibrated. You can check that with intensity profiles (line & CTRL+K) or histograms. For the x-y scale, use Analyze/set scale.

@Nicolas, you are magic!!! It is right.
How can I save 3D image as .tiff or .stl format? So, after these manipulations, I want to simulate the 3D model. It is real to get a .stl file?

Hello @zekan96,
sorry for the delay. You can save the image as TIF (File/Save as…), the scales will be preserved. Unfortunately, I don’t know of a method for converting height images into STL with FIJI straightforwardly. By the way, if anyone knows more about that, please let me know.
I see two options:

  • convert your height image into a binary stack, then convert the stack into STL using BoneJ (
  • import the height file as a point cloud (XYZ file) into another software such as Meshlab and mesh it.

Please note that both of these options will give you a mesh covering your surface only. I don’t know how you intend to simulate it, but most probably you’ll need a volumetric mesh with points under your surface.

Good day, @Nicolas,
sorry for the delay too. I try to repeat your advice tomorrow. I surely will answer!

Thank you for large and long help!

Hello All,
In Plugins > 3D IO there is an option for export to STL and seems to work great for me.

1 Like

Good evening!
Sorry for missing.
@Nicolas and @smith_robertj, I tried your advice and got the best results. Thank you!