I created several microstructures and took electron microscope pictures at a 45 degree tilt at all 360 degrees around the structure. I want to convert these images into a single 3d model of the structure but both ReMake and VisualFSM can't seem to do it (I think the contrast is too low). Is there a way to manually (or automatically) create a 3d model from these pictures??
Sometimes Blender is not the tool. As stated in the comments there are external tools dedicated to processing the described (detailed) input into the desired output. When these tools produce a file format that Blender can read, that's how you get the data into Blender.
This is not an endorsement of 3rd party software
Software like Agisoft Photoscan offers a python interface to let you sidestep the ui for automation purposes - but it's out of the realm of Blender support to discuss that unless there is a concrete question about interactivity between the two programs or APIs.