Build A Brain
###Automate the Comparing of Image Values to Reverse Engineer Dinosaur Brains
####Background
A current research project at the museum is rebuilding the brain structures from reverse casts of the interiors of fossil skulls. This is done manually by visually checking greyscale values in many hundreds of CT scan TIFF image files. Expensive proprietary software is currently being used to build these 3D models based on the image stacks. Automation of this process could save incredible amounts of time and rapidly advance the state of the research. Is it possible to use machine learning, machine vision, medical imaging advances to address this?
####Solutions
- Software or scripts which may enhance local contrast of images in stack to improve edge detection (say between bone and deposited rock)
- Making a 3D model of just the skull without air or sedimentary rock surrounding the skull (turning the TIFF image stack into .stl files)
- Based on skull reconstruction model, create the reverse cast and output an STL
- EXTRA CREDIT - understand VGL file format (XML?) and output a "rough draft" in VGL file
####Resources
- Example video of brain reconstruction
- Information about the AMNH CT scanner
- GE Phoenix CT scanner
- myVGL viewer - freely available software to view vg project files
- Description of manual process with examples of how it is currently done
- Screen capture of VG studio showing outline of bone manually created by human
- CT image stacks
- ImageJ2 - used to enhance contrast in grayscale images, could be useful for many aspects of solutions for this challenge
