Monday, July 28, 2014

Interlude: CT Scanning Microfossils

CT-Scanning Process
One aspect of our work this summer is creating 3D images of some of our specimens. This can be accomplished non-destructively with the CT (Computed Tomography) scanner down the hallway in the Micro-Imaging Facility.
GE Phoenix Vtomexs
GE Phoenix CT-Scanner (photo credit:
Before we scan a specimen, we mount it in the tip of a micropipette and place it inside the CT-scanner. The specimen is mounted between an x-ray source, which shoots x-rays at the sample, and a detector. Much like a camera, which creates an image based on how much light enters through a lens, the CT-scanner creates images based on how many x-rays reach a detector. Dark spots in the image mean that x-rays traveled directly from source to detector; brighter spots appear where the x-rays passed through denser materials.
AMNH-FI-87587 Uvigerina strata
To obtain a 3D image, the x-ray source remains stationary while the sample rotates. While the specimen rotates, the scanner gathers data at set intervals, ultimately producing more than a thousand images. This process can take anywhere between 30 minutes and 2 hours. At the end of the scan, we transfer the raw data (over a thousand high-quality images and other proprietary files) onto a hard drive. While the CT scanner's job is now complete, the intern's work is never over.

CT-Scan Processing

Cleaning up a CT scan and sectioning it

We use software created by the scanner's manufacturer to reconstruct a volume from a series of 2D images. Then, we edit this volume in VG Studio. Because the mounting materials are denser than air, there is usually unwanted noise in the scan. Sometimes removing all of this noise to isolate the fossil can be a very time-consuming process.
Region Growing in VG Studio
After isolating the specimen, we create videos and interactive files showing internal and external 3D structure. We can even send our processed CT scan data to one of the museum's 3D printers! 
gif of the CT scan of AMNH-FI 87934 Cibicides fletcheri

A 3D-printed Foram!

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