University of Washington Researchers use Amira Software Towards Aiding the Pathology of Pancreatic Cancer
For nearly 100 years, pathology for cancer diagnosis has involved a standard, but complex series of steps to process tissue biopsies procured from a patient in the clinic. Many procedures are a direct result of the fact that observation and evaluation of specimens by pathologists occur using a standard microscope (in 2D).
In 2014, the Human Photonics Laboratory at the University of Washington demonstrated that the rudimentary operations of a pathology laboratory may be replicated on whole, unsectioned tissue biopsies using microfluidics within a credit card-sized device . The device may potentially reduce the entire pathology laboratory's infrastructure and physical footprint for 3D optical imaging of tissue biopsies 1-3 . Imaging tissue biopsies (in 3D) makes utility of the entire patient specimen prior to sectioning, provides a fundamental gain in optical (diagnostic) data, and may permit initial biopsy triage and evaluation within the workflow of traditional pathology.
A pancreas core biopsy was obtained using a clinical needle and (a) was imaged in 3D using white light and our 3D microscope 4 . The optical data acquired were then processed to produce (b) a basic 3D reconstruction, where (c) isolated regions of the biopsy were rotated, magnified and inverted (in color) to aid pathologists in biopsy evaluation. Limitations of basic reconstruction software packages include data size and rendering. For example, the (b) reconstruction is not only highly reduced in size with respect to the (a) original dataset, but it also only displays the (d) surface of the biopsy at low resolution. Amira software permits our original optical dataset to be (e) completely loaded into its software package at full resolution, where object manipulation is easy and rapid for initial tissue interrogation studies. The software additionally (f) renders the entire volume of the biopsy and allows our team to threshold the reconstructed data for specific investigations involving whole tissue staining.
The goal of the Human Photonics Laboratory (HPL) at the University of Washington (Seattle) is to advance the frontier of optical technology in the areas of cancer detection and treatment.
Amira and Avizo are high-performance 3D software for visualizing, analyzing, and understanding scientific and industrial data coming from all types of sources and modalities.
Images and text are courtesy of HPL
1. R Das, CW Burfeind, GM Kramer, EJ Seibel. Pathology in a tube: Step 1. Fixing, staining, and transporting pancreatic core biopsies in a microfluidic device for 3D imaging. Microfluidics, BioMEMS, and Medical Microsystems XII, Proceedings of SPIE 8976:89760R (2014).
2. R Das, A Agrawal, MP Upton, EJ Seibel. Optically clearing tissue as an initial step for 3D imaging of core biopsies to diagnose pancreatic cancer. Optical Interactions with Tissue and Cells XXV and Terahertz for Biomedical Applications, Proceedings of SPIE 8941:89410N (2014).
3. R Das, TM Nguyen, SD Lim, M O'Donnell, RK Wang, EJ Seibel. Feasibility of a hybrid elastographic-microfluidic device to rapidly process and assess pancreatic cancer biopsies for pathologists. IEEE-EMBS Health Innov Point Care 271-275 (2014).
4. R Das, RG Murphy, EJ Seibel. Beyond isolated cells: microfluidic transport of large tissue for pancreatic cancer diagnosis. Proc SPIE Int Soc Opt Eng 9320:93200N (2015).