3D Reconstruction using JPEG

Hi All,
I want to reconstruct a dog skull starting from 39 JPEG extracted from TC exam.
At the moment I can’t reach the DICOM files.

I uploaded the images in Fiji but i think I haven’t a sufficient number of slices. Slice thickness is 2mm.
I attach the 3D viewer view.

Any idea?

Thank you

Hi @Mezza35

As you said, your slices are 2mm thick, this means your voxels have a depth of 2mm. I assume that the x-y-resolution of your images is much better (<2mm). But the default assumption is, that voxels are isotropic (1x1x1). You can change that via Image -> Properties.

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Here we are the properties:

@Mezza35 apparently I saved my comment with two “<”-signs and the formatting went really bad.

Could you kindly better explain?
I didn’t understand.

Thank you

Sure :slight_smile:

A 2D image consists of pixels, which are usually quadratic. Let’s assume one pixel represents an area of 0.1x0.1mm of your real object. If you have a higher resolution this area gets smaller.
In a 3D image the pixels are called voxels (a combination of volumetric and pixel). Most of the time the depth resolution is not as good as the x-y-resolution. This is due to the fact that you take image slices (2D images) and combine them to a 3D stack. As you said, your slices have a thickness of 2mm, now you have to figure out what the x-y-resolution of your images is. Let’s assume it is 0.1x0.1mm. Which means that the relative size of your voxels is 0.1x0.1x2. But the default assumption is that voxels are isotropic (1x1x1). You can change the voxel size via the menu “Image -> Properties…”.

Thank you!

I attach one example of the 39 JPEG. In your opinion, what is x-y-resolution?
Now i can use the plugin “3D Viewer” but i cant’ reconstruct the different tissues.
What plugin did you suggest?

Thank you


I can’t tell you the resolution from looking at the picture. Usually the resolution is part of the meta-data or you can find it in the camera specs.

What do you mean by reconstruct?
If you would like to make a binary mask you can apply a threshold and convert it later to a 3D mesh if needed.

I’m sorry, i don’t have the camera specs, i have only the JPEG.

I want to extract from this JPEG the mesh of the skull, but i think it isn’t possible:
with DICOM file I can extract skull using Hunsfield Unit, but i don’t think I can extract this info from JPEG.

Thank you

From your image it seems the pixel size should be 239.48/505 = 0.474 mm/pixel. Try setting that number in the image properties (Image > Properties…, Pixel width and Pixel height) and then call the 3D viewer.