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3D imaging and modeling pipeline for student researchers

Department of Biology








The development of three-dimensional (3D) imaging has revolutionized research and education by allowing the visualization and modeling of complex structures. Within biology, medicine, and engineering, 3D technology enables researchers to study biological and non-biological structures and construct detailed models of how these structures function. Although there are imaging facilities and workstations at UW, substantial technical limitations are preventing student researchers from making full use of these facilities, particularly within the biological sciences. First, there is a shortage of high-performance software capable of visualizing and processing complex 3D data, and integrating these data into mathematical modeling/simulations to investigate scientific questions. Open source alternatives exist, but are highly limited in performance and functionality. Second, there is a lack of imaging technologies that allow students to efficiently generate large 3D datasets, particularly for structures or objects in the order of a few centimeters in size. The currently available micro-Computed Tomography scanning facilities allow students to image internal anatomy in high resolution, but these procedures are highly time consuming and labor intensive for the purposes of imaging external shapes. All of these limitations have created an acute need for a high-throughput and user-friendly pipeline to image and model 3D objects, which can be easily accessed by students for research and training. Our proposal seeks funding to purchase three components that will form this pipeline: an AutoScan Inspec scanner for capturing 3D images, Amira Pro software for visualizing and processing 3D images, and COMSOL Multiphysics software for conducting physical simulations on 3D objects.


Users will email the PI/student leads, who will provide access to a Google calendar where they can book a training session, time on the computers with the software for either in-person or remote use, as well as use of the scanner.

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Learn about the Student Technology Fee and the proposal process by attending a Workshop led by our staff and receive 1:1 support with your proposal.


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