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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Abstract	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.
AbstractList	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. 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.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. Abstract 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.
Author	Terebes, Romulus Belean, Bogdan Le Gal, Bertrand Borda, Monica
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Cites_doi	10.1109/TCBB.2006.3 10.1109/TMI.2008.915697 10.1109/TNB.2003.817023 10.1007/11679363_89 10.1007/978-3-540-85567-5_41 10.1016/j.ins.2006.07.004 10.1109/TPAMI.1986.4767851 10.1186/1471-2105-11-49 10.1093/bioinformatics/btg057 10.1187/cbe.07-05-0028 10.1016/j.compmedimag.2009.09.005 10.1155/ASP/2006/80163 10.1109/TMI.2008.915561 10.1186/1471-2105-12-113 10.1093/bioinformatics/17.7.634 10.3844/ajassp.2006.1730.1734 10.1109/TIP.2003.819941
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Keywords	Parallel computation Image processing Microarray Gene expression FPGA technology
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Snippet	Automation is an open subject in DNA microarray image processing, aiming reliable gene expression estimation. The paper presents a novel shock filter based... Abstract Automation is an open subject in DNA microarray image processing, aiming reliable gene expression estimation. The paper presents a novel shock filter...
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SubjectTerms	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
Title	FPGA based system for automatic cDNA microarray image processing
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