cDNA Microarray Image Enhancement for Effective Gridding of Spots

Joseph, Steffy Maria; Sathidevi, P. S.

doi:10.1109/tencon.2019.8929512

Cited by 6 publications

(5 citation statements)

References 9 publications

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“…Since SMD [2] is not available for our work, we neglected the comparison of SMD's results in local gridding results and discussion. The resultant figures after the global gridding are exhibited in Fig.…”

Section: Tablementioning

confidence: 99%

“…cDNA microarray image analysis is an important part of microarray experimental studies that can potentially have a significant impact on subsequent analyzes such as clustering or detection of differential genes [1]. The basics of DNA, cDNA, DNA chips and cDNA microarray image formation are described in our earlier work [2]. A comprehensive virtual laboratory experiment is available in [3], by which we can investigate the differences between healthy cells and cancer cells using DNA microarray.…”

Section: Introductionmentioning

confidence: 99%

“…However, they only gave the local gridding results of that dataset. SMD [1] used in our work is different from SMD [2] used in the literature. Both are SMD microarray databases with different numbers of sub-arrays, spots, and other features.…”

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confidence: 99%

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A Fully Automated Gridding Technique for Real Composite cDNA Microarray Images

Joseph

Sathidevi

2020

IEEE Access

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Genome-wide screening using microarrays of DNA will be of great use in the early diagnosis of diseases such as cancer and HIV. It also makes use of gene discovery, pharmacogenomics, toxicogenomics, and nutrigenomics for other applications. A DNA microarray image lays out an orderly arranged specific gene regions called spots. Microarray image analysis consists primarily of preprocessing, spot area gridding, spot segmentation, and intensity extraction. The first two phases are focused on this work: preprocessing and gridding. The experiment is conducted on real composite cDNA microarray images. A composite microarray image is formed by suitably stacking a red channel image and a green channel image acquired from a microarray experiment either in the RGB domain or in the GRB domain. The blue channel is kept as zero. In order to reduce the challenging problems of microarray images, an efficient preprocessing algorithm is proposed here for these composite images. We have developed a fully automated gridding algorithm integrating global subgrid gridding and local gridding of spots. This technique extracts the structural information namely inter-subgrid spacing, inter-spot spacing and spot center position to achieve efficient gridding. The traits of a microarray image are evaluated using three parameters namely Mean square error, Naturalness quality image evaluator and degree of contrast. The accuracy of the experimental results indicates that this combined preprocessing and gridding technique performs better than existing competitive methods in SIB, GEO, SMD and DeRisi datasets which are most commonly used by the research community for microarray image analysis techniques. INDEX TERMS cDNA, composite microarray images, contrast enhancement, denoising, fully automated gridding, genome-wide monitoring, global gridding, hybridized spots and non-hybridized spots, local gridding, spot region extraction.

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Section: Tablementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Fully Automated Gridding Technique for Real Composite cDNA Microarray Images

Joseph

Sathidevi

2020

IEEE Access

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“…In the following, some of the solutions that the researchers used in their works will be presented. In paper [6] the Sauvola method was applied for adaptive photo binarization, while in paper [7] and [8] the Otsu method was used to solve the problem of binarization. Also, in the paper [8] the problems of removing smudges and rotation of the display were considered.…”

Section: Introductionmentioning

confidence: 99%

“…In paper [6] the Sauvola method was applied for adaptive photo binarization, while in paper [7] and [8] the Otsu method was used to solve the problem of binarization. Also, in the paper [8] the problems of removing smudges and rotation of the display were considered. Methods for solving the problem of photo rotation are presented in [9] and [10].…”

Section: Introductionmentioning

confidence: 99%

Problems of software processing of acquired rotor intended for determining required dimensions

Turinski,

Svalina,

Lujić

et al. 2023

Acta IMEKO

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Some of the problems that arise during image processing are analysed in this paper. The most commonly used software tools in image processing require binary photography, and its conversion into the binary form is required first. Conversion problems, and their proper solution, are key steps for further machine determination of product dimensions. Removing smudges on binary photos and rotating displays for photo overlap methods are the problems that are solved in the present work, in order to successfully prepare the photo with software for further determination of product dimensions. The knowledge gained in this paper will help scientists and facilitate their software preparation and processing of the photo used to determine the required dimensions of the product.

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