Others on the forum that are more familiar with histology data can chime in. 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). I think ImageJ has a specific function to do that. You can try to register one slide to the next one and keep moving in the stack. If you move up and down in the red slice view, you will see the tissue rotating from one slide to the next). This page is the official homepage for 3D Object Converter, a powerful 3D polygon model translation and interactive viewing shareware tool that allows arbitrary 3D model data to be imported from external sources, exported to various industry standard 3D file formats with great accuracy and quality. (see the jagged edges in green and yellow slice. Hence, you will not get a good volume rendering out of these, because when stacked together they do not constitute a proper 3D ‘volume’. However, slides are not co-registered i.e., the orientation of the tissue is different from one slide to the next. 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. 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?
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