Fiji Micro CT import

Hello everybody,

I am trying to import micro CT images (DICOM format) into Fiji. Import image sequence will let me import the dcm files, but unfortunately I can’t change the threshold or do a surface renderings/3D Viewer all menus greyed out. What is the best workflow for importing and manipulating Micro CT images ? BoneJ was mentioned as a relevant plugin in some forums, but als there I couldn’t find a way to create surfaces and export them. Which is what I am trying to achieve. Or maybe there is some other free software that is better suited to achieve this. Any help would be great.

Thank you.


my guess is the menus are grayed out because nothing is selected. If you click on your volume, it should become selected (indicated by a red frame) and the corresponding menu items should become enabled.

Best, Bene

Thank you for the answer, after selecting and deselecting it a couple of times finally it showed the Volume (which was a bit odd). Now if I try to do the same with a surface it takes a very long time and then runs out of memory. I increased the memory to 12 GB (16 GB Total), the stack is 507 images, 8 bit and 127 MB (500x512px). My laptop is not too bad, the same task with another software and e.g. 1000 images is done in seconds (not Micro CT). How can Fiji use 800 % of the CPU and with all this RAM still crash.

What am I doing wrong ? Is there a smart way to do this ? Maybe in steps. Or are these Micro CT higher much resolution images ? I don’t get why it always crashes.
Or should I segment it before loading it into the 3D Viewer.

Thanks and sorry for all the questions.

Using Virtual Stack works better.

But I would still like to know what an ideal workflow to import images and extract surfaces would be without using too much RAM/or using it efficiently.
For example if I start the 3D Viewer it asks me about three color channels, even if I convert to greyscale before. If I uncheck those boxes it takes even longer. It just seems to take a very long time.

How can I reduce this time (even if I reduce the quality of the resulting surface a bit) or split the process in parts. Anything that could achieve this would be very interesting.