FPGA based system for automatic cDNA microarray image processing

Automation is an open subject in DNA microarray image processing, aiming reliable gene expression estimation. The paper presents a novel shock filter based approach for automatic microarray grid alignment. The proposed method brings up significantly reduced computational complexity compared to state...

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Vydáno v:Computerized medical imaging and graphics Ročník 36; číslo 5; s. 419 - 429
Hlavní autoři: Belean, Bogdan, Borda, Monica, Le Gal, Bertrand, Terebes, Romulus
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Elsevier Ltd 01.07.2012
Elsevier
Témata:
Algorithms
Automated
Automation
Computation
Cost analysis
Engineering Sciences
Field programmable gate arrays
FPGA technology
Gene expression
Hardware
Image Enhancement - methods
Image Interpretation, Computer-Assisted - methods
Image processing
In Situ Hybridization, Fluorescence - methods
Internal Medicine
Micro and nanotechnologies
Microarray
Microelectronics
Microscopy, Fluorescence - methods
Oligonucleotide Array Sequence Analysis - methods
Other
Parallel computation
Pattern Recognition, Automated - methods
Reproducibility of Results
Sensitivity and Specificity
Parallel computation
Image processing
Microarray
Gene expression
FPGA technology
ISSN:0895-6111, 1879-0771, 1879-0771
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Popis
Shrnutí:Automation is an open subject in DNA microarray image processing, aiming reliable gene expression estimation. The paper presents a novel shock filter based approach for automatic microarray grid alignment. The proposed method brings up significantly reduced computational complexity compared to state of the art approaches, while similar results in terms of accuracy are achieved. Based on this approach, we also propose an FPGA based system for microarray image analysis that eliminates the shortcomings of existing software platforms: user intervention, increased computational time and cost. Our system includes application-specific architectures which involve algorithm parallelization, aiming fast and automated cDNA microarray image processing. The proposed automated image processing chain is implemented both on a general purpose processor and using the developed hardware architectures as co-processors in a FPGA based system. The comparative results included in the last section show that an important gain in terms of computational time is obtained using hardware based implementations.
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ISSN:0895-6111
1879-0771
1879-0771
DOI:10.1016/j.compmedimag.2012.01.002