i am new to 3d slicer and i have a set of image slices (2D), which are from a probe cut in 100 um steps, and i want to put these images together and do a 3d model. What steps do I need to follow to create a 3D reconstruction from 2D image slices using 3D Slicer, and how can I ensure that the final model retains the colors of the original images so that I can view it in 3D?
I saw a lot of tutorials but im still getting a wrong 3d model when im doing volume rendering. I can upload the images
I uploaded the images in case anyone wants to take a look on them
These are histology slides (I think), so if you simply uncheck the “grayscale” option in the ImageStacks module of SlicerMorph, you will get color (RGB) images. However, slides are not co-registered; i.e., the orientation of the tissue is different from one slide to the next. Hence, you will not get a good volume rendering out of these, because when stacked together they do not constitute a proper 3D ‘volume’. (see the jagged edges in green and yellow slice. If you move up and down in the red slice view, you will see the tissue rotating from one slide to the next).
You can try to register one slide to the next one and keep moving in the stack. I think ImageJ has a specific function to do that. I am not sure if there is anything in the Slicer to help you in aligning the slides (there a lots of registration tools, but they are usually for registering one 3D volume to another). Others on the forum that are more familiar with histology data can chime in.
I didn’t do anything. I simply dragged one of your files into Slicer and asked it to open with ImageStacks. However, your files are not named conventionally. Normally slice sequences go something like 0001, 0002, 0003, and yours are missing leading zeros. Your operating systems may sort those files differently then mine (MacOS). Please expand the files list and see that the sequence of files is correst (ie., it goes 1,2,3,…,10,11,12,…100,101).
Imagestack relies on the ordering OS provides and we expect the files to have properly formated sequences.
thank you again, i tried now to rename the files as you said, and im still not getting the same 3d Model, it seems that the software is still taking the images in a different order because i did exactly the same as you said, do you have any other ideas why this is happening? (Screenshot)
im sorry from the first look, i thought that your 3d model was different and didnt have this rough transitions between the layers, my goal is to make these transitions between the layers as smooth as possible.
This is feasible to the extend that these slides do not have large gaps between them, i.e., the sections are sufficiently sampled. Are you sure the spacing between slides is the same as the in-plane spacing (0.1 mm). In my experience they are usually least an order of magnitude larger. Yes, jagged edges will probably be less jagged if you include more slides (but they also need to be correctly registered) and used the correct spacing.
I don’t think you are doing anything wrong. You just need to find a registration algorithm that will do a better slice-to-slice registration. I highlighted one slide that’s obviously quite offset with respect to the others. The others are like that, but not as obvious.