Automatic Bone Measurement from X-Ray Computed Tomography

Hall, Alexander S.

Thermo Fisher Scientific

Houston, TX

alex.hall@thermofisher.com

Department of Biology

The University of Texas at Arlington

Arlington, TX

Jacobs, Justin

Smith, Eric N.

Department of Biology

The University of Texas at Arlington

Arlington, TX

Analyzing three-dimensional data often requires slow and tedious manual decision making by a trained user. Traditionally, decisions about what belongs to a material are made layer-by-layer for every single image in a z-stack of hundreds or thousands of images. For example, digitally extracting one single bone from a complete skeleton is often the most time consuming portion of comparative morphology projects. Using X-ray computed tomography (CT) data with sufficient information about biologically real boundaries (sutures, joints, etc.), one can use professional CT segmentation software to automatically segment skeletons. In this project, I report a new workflow using an object separation process within Thermo Scientific Amira-Avizo Software. After optimizing the object separation parameters, individual bones were isolated and measured with only a fraction of the work required by manually selecting bones layer by layer. I will present a use case where I studied a CT data from a snake skeleton at the single-bone level leading to the discovery of a bone cancer (i.e,. osteosarcoma). The workflow should assist with achieving a semi-automated way to analyze anatomical CT data, including in lizards.


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