Some recent tests using 3D Zephyr free software to compile a set of images into a 3D composite. The resulting images would need a bit more work to either be used in creating a virtual 3d fungi environment, or even to be printed. The software has done an amazing job considering there were only 9 images and the minimum amount of images I would recommend is around 50.
The software is free but you are limited to 50 images and you can only export to Sketchfab. Thfe paid version of the software does not have these limitations.