I managed to create a 3D reconstruction out of 2D histology slices but I’m having trouble with transparency. Basically, the organs that I want to visualised are “inside” the 3D object, meaning that there are slices on the foreground that are blocking them from view (since the slices are opaque images). Is there are a way to adjust the transparency of the slices so that the sections at the front are less opaque, and the sections where the organs appear overlap with each other creating a shape/outline? I have kind of managed to make it work by playing with the opacity slider in the volume rendering module but it creates blurry/incomplete results.
In case it helps, what I’ve done is align the individual slices with TrakEM2, then load those as a single object on 3Dslicer, make a scalar volume and then use the volume rendering module (basically followed the video tutorial on youtube). The presets on the volume rendering are all related to human body parts so those don’t work for me (I’m using sections from a worm).
Thank you in advance.