An abstract virtual instrument system for high throughput automatic microscopy

Russel, A. B. M., Abramson, David, Bethwaite, Blair, Minh Ngoc Dinh, Enticott, Colin, Firth, Stephen, Garic, Slavisa, Harper, Ian, Lackmann, Martin, Schek, Stefan and Vail, Mary (2010). An abstract virtual instrument system for high throughput automatic microscopy. In: Iccs 2010 - International Conference On Computational Science, Proceedings. 10th International Conference on Computational Science, ICCS 2010, Amsterdam, Netherlands, (545-554). 31 May-02 June 2010. doi:10.1016/j.procs.2010.04.058

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Author Russel, A. B. M.
Abramson, David
Bethwaite, Blair
Minh Ngoc Dinh
Enticott, Colin
Firth, Stephen
Garic, Slavisa
Harper, Ian
Lackmann, Martin
Schek, Stefan
Vail, Mary
Title of paper An abstract virtual instrument system for high throughput automatic microscopy
Conference name 10th International Conference on Computational Science, ICCS 2010
Conference location Amsterdam, Netherlands
Conference dates 31 May-02 June 2010
Proceedings title Iccs 2010 - International Conference On Computational Science, Proceedings   Check publisher's open access policy
Journal name Procedia Computer Science   Check publisher's open access policy
Place of Publication Amsterdam, The Netherlands
Publisher Elsevier BV
Publication Year 2010
Year available 2010
Sub-type Fully published paper
DOI 10.1016/j.procs.2010.04.058
Open Access Status Not Open Access
ISSN 1877-0509
Volume 1
Issue 1
Start page 545
End page 554
Total pages 10
Language eng
Formatted Abstract/Summary
Modern biomedical therapies often involve disease specific drug development and may require observing cells at a very high resolution. Existing commercial microscopes behave very much like their traditional counterparts, where a user controls the microscope and chooses the areas of interest manually on a given specimen scan. This mode of discovery is suited to problems where it is easy for a user to draw a conclusion from observations by finding a small number of areas that might require further investigation. However, observations by an expert can be very time consuming and error prone when there are a large number of potential areas of interest (such as cells or vessels in a tumour), and compute intensive image processing is required to analyse them. In this paper, we propose an Abstract Virtual Instrument (AVI) system for accelerating scientific discovery. An AVI system is a novel software architecture for building an hierarchical scientific instrument - one in which a virtual instrument could be defined in terms of other physical instruments, and in which significant processing is required in producing the illusion of a single virtual scientific discovery instrument. We show that an AVI can be implemented using existing scientific workflow tools that both control the microscope and perform image analysis operations. The resulting solution is a flexible and powerful system for performing dynamic high throughput automatic microscopy. We illustrate the system using a case study that involves searching for blood vessels in an optical tissue scan, and automatically instructing the microscope to rescan these vessels at higher resolution.
Keyword Abstract Virtual Instrument System
Scientific Workflows
Automatic Microscopy
Grid Computing
Cancer Research
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status Non-UQ

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