Stack to Projection -- 3D Projection

Hello all, I have a two-part question:

  1. In 3D Projection (Stack to Projection), “Slice spacing” is sometimes given in pixels, e.g. Slice spacing (pixels): 100". However, in the version of Fiji that I have downloaded, “Slice spacing” is given in inches. How do I change this to pixels? Is it even possible? There is no drop-down menu for you to choose from. It’s in inches and that’s it. But I want it in pixels.

  2. I want to make a 3D projection of 200 images. So I choose Projection Method as “brightest point”, axis of rotation as “y axis”, slice spacing as 1 inch (when what I would really like is slice spacing of 100 pixels), surface depth cueing at 50, etc etc, and then I tick the Interpolate box. Problem is, when I click OK, the software takes HOURS to process my request. At the end of 8.5 hours or whatever it was, Fiji just closed on its own accord. And this has happened over MANY weeks. When I uploaded 8 images into Fiji (and not 200) and ran the 3D projection, it still took some time (35 minutes), but the 3D video WAS successfully created. But with 200 images, no way. Is there any way around this? I have increased the MEMORY on Fiji, but still it won’t process 200 images. Any advice please?

Hi Tigve,

I guess the issue is not coming from your FIJI but from reading the metadata of your image.
You can force the correct value, or set to pixel, in Image > Properties.

Please find below a macro code that does it for the mitosis sample :

run("Mitosis (26MB, 5D stack)");

run("Properties...", "channels=2 slices=5 frames=51 unit=micron pixel_width=1 pixel_height=1 voxel_depth=1 frame=[0.14 sec]");

run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=1 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=100 interior=50");



Hello Romain,

Thank you kindly – that was really helpful information.