{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,14]],"date-time":"2025-10-14T06:41:03Z","timestamp":1760424063873,"version":"build-2065373602"},"reference-count":54,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T00:00:00Z","timestamp":1496880000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the National Science Foundation of China","award":["Nos. 61665012 and 61575168"],"award-info":[{"award-number":["Nos. 61665012 and 61575168"]}]},{"name":"the International Science and technology cooperation project of Ministry of Education of the People's Republic of China","award":["2014-2029 and 2016-2196"],"award-info":[{"award-number":["2014-2029 and 2016-2196"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>A new method for extracting the dots is proposed by the reflected light image of porous silicon (PSi) microarray utilization in this paper. The method consists of three parts: pretreatment, tilt correction and spot segmentation. First, based on the characteristics of different components in HSV (Hue, Saturation, Value) space, a special pretreatment is proposed for the reflected light image to obtain the contour edges of the array cells in the image. Second, through the geometric relationship of the target object between the initial external rectangle and the minimum bounding rectangle (MBR), a new tilt correction algorithm based on the MBR is proposed to adjust the image. Third, based on the specific requirements of the reflected light image segmentation, the array cells are segmented into dots as large as possible and the distance between the dots is equal in the corrected image. Experimental results show that the pretreatment part of this method can effectively avoid the influence of complex background and complete the binarization processing of the image. The tilt correction algorithm has a shorter computation time, which makes it highly suitable for tilt correction of reflected light images. The segmentation algorithm makes the dots in a regular arrangement, excludes the edges and the bright spots. This method could be utilized in the fast, accurate and automatic dots extraction of the PSi microarray reflected light image.<\/jats:p>","DOI":"10.3390\/s17061335","type":"journal-article","created":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T10:26:09Z","timestamp":1496917569000},"page":"1335","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Image Processing of Porous Silicon Microarray in Refractive Index Change Detection"],"prefix":"10.3390","volume":"17","author":[{"given":"Zhiqing","family":"Guo","sequence":"first","affiliation":[{"name":"College of Information Science and Engineering, Xinjiang University, Urumqi 830046, China"}]},{"given":"Zhenhong","family":"Jia","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Xinjiang University, Urumqi 830046, China"}]},{"given":"Jie","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China"}]},{"given":"Nikola","family":"Kasabov","sequence":"additional","affiliation":[{"name":"Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1020, New Zealand"}]},{"given":"Chuanxi","family":"Li","sequence":"additional","affiliation":[{"name":"School of Physical Science and Technology, Xinjiang University, Urumqi 830046, China"}]}],"member":"1968","published-online":{"date-parts":[[2017,6,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1126\/science.1990438","article-title":"Light-directed, spatially addressable parallel chemical synthesis","volume":"251","author":"Fodor","year":"1991","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev.bioeng.4.020702.153438","article-title":"DNA microarray technology: Devices, systems, and applications","volume":"4","author":"Heller","year":"2002","journal-title":"Annu. Rev. Biomed. Eng."},{"key":"ref_3","first-page":"119","article-title":"Monitoring gene expression using DNA arrays","volume":"71","author":"Ali","year":"2003","journal-title":"Methods Mol. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1063\/1.2432247","article-title":"Fluorescent polymer-porous silicon microcavity devices for explosive detection","volume":"90","author":"Levitsky","year":"2007","journal-title":"Appl. Phys. Lett."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/nm0103-140","article-title":"Trends in microarray analysis","volume":"9","author":"Stears","year":"2003","journal-title":"Nat. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.bios.2014.11.042","article-title":"OLED-based DNA biochip for Campylobacter spp. detection in poultry meat samples","volume":"66","author":"Manzano","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_7","unstructured":"Chiang, Y.Z., Zhao, C., and Melbourne, W. (2015, January 19). Biochip immunofluorescence microscopy as a new diagnostic tool for autoimmune blistering skin diseases in Australia. Proceedings of the Meeting of the Medical-Dermatology-Society, San Francisco, CA, USA."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4934","DOI":"10.1039\/C4AN00687A","article-title":"A novel biosensor array with a wheel-like pattern for glucose, lactate and choline based on electrochemiluminescence imaging","volume":"139","author":"Zhou","year":"2014","journal-title":"Analyst"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1016\/j.snb.2011.10.016","article-title":"A newly developed optical biochip for bacteria detection hybridization","volume":"161","author":"Yeh","year":"2012","journal-title":"Sens. Actuators B Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"036002","DOI":"10.1117\/1.JBO.17.3.036002","article-title":"Polarization Interferometry Based Wavelength-Interrogation Surface Plasmon Resonance Imager for Analysis of Microarrays","volume":"11","author":"Liu","year":"2012","journal-title":"J. Biomed. Opt."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Li, Y., Ma, X., Zhao, M., Qi, P., and Zhong, J. (2014). Quick and Label-Free Detection for Coumaphos by Using Surface Plasmon Resonance Biochip. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0104689"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s11433-013-5384-y","article-title":"Label-free high-throughput and real-time detections of protein interactions by oblique-incidence reflectivity difference method","volume":"57","author":"He","year":"2014","journal-title":"Sci. China Phys. Mech. Astron."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5569","DOI":"10.1109\/JSEN.2015.2441651","article-title":"An Analysis and Design of Photonic Crystal-Based Biochip for Detection of Glycosuria","volume":"15","author":"Sharma","year":"2015","journal-title":"IEEE Sens. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.optcom.2015.05.049","article-title":"Centroid shift analysis of microlens array detector in interference imaging system","volume":"354","author":"Zhao","year":"2015","journal-title":"Opt. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/j.bios.2015.11.050","article-title":"Establishment of N-succinimidyl 4-(maleimidomethyl) cyclohexanecarboxylate (SMCC) modified biochip enabling concurrent detection of serum infectious antibodies in neuroborreliosis","volume":"78","author":"Ye","year":"2016","journal-title":"Biosens. Bioelectron."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.talanta.2014.11.023","article-title":"Gold nanorod biochip functionalization by antibody thiolation","volume":"136","author":"Xuefeng","year":"2015","journal-title":"Talanta"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Kim, M.I., Park, T.J., Paskaleva, E.E., Sun, F., Seo, J.W., and Mehta, K.K. (2015). Nanotechnologies for Biosensor and Biochip. J. Nanomater., 420734.","DOI":"10.1155\/2015\/420734"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"966","DOI":"10.4028\/www.scientific.net\/AMR.694-697.966","article-title":"Simulation of gold nanoparticles aggravating MEMS cantilever optical static detection Biochip","volume":"694\u2013697","author":"Ge","year":"2013","journal-title":"Adv. Mater. Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.jelechem.2015.08.015","article-title":"Microfluidic multiplex biochip based on a point-of-care electrochemical detection system for matrix metalloproteinases","volume":"756","author":"Hwang","year":"2015","journal-title":"J. Electroanal. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Schmidt, S., Flueckiger, J., Wu, W., Grist, S.M., Talebi Fard, S., Donzella, V., Khumwan, P., Thompson, E.R., Wang, Q., and Kulik, P. (2014, January 14\u201317). Improving the performance of silicon photonic rings, disks, and Bragg gratings for use in label-free biosensing. Proceedings of the SPIE\u2014The International Society for Optical Engineering, Bruxelles, France.","DOI":"10.1117\/12.2062389"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4791","DOI":"10.1364\/OE.23.004791","article-title":"Design and fabrication of SOI micro-ring resonators based on sub-wavelength grating waveguides","volume":"23","author":"Donzella","year":"2015","journal-title":"Opt. Express"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Li, C., Jia, Z., Li, P., Wen, H., Lv, G., and Huang, X. (2017). Parallel Detection of Refractive Index Changes in a Porous Silicon Microarray Based on Digital Images. Sensors, 17.","DOI":"10.3390\/s17040750"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00340-016-6405-0","article-title":"Refractive index change detection based on porous silicon microarray","volume":"122","author":"Chen","year":"2016","journal-title":"Appl. Phys. B"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.snb.2006.02.002","article-title":"Improved surface sensing of DNA on gas-etched porous silicon","volume":"120","author":"Tessier","year":"2006","journal-title":"Sens. Actuators B"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.bios.2013.01.012","article-title":"Porous silicon optical microcavity biosensor on silicon-on-insulator wafer for sensitive DNA detection","volume":"44","author":"Zhang","year":"2013","journal-title":"Biosens. Bioelectron."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1016\/j.talanta.2006.05.089","article-title":"Porous silicon as functionalized material for immunosensor application","volume":"71","author":"Meskini","year":"2007","journal-title":"Talanta"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1063\/1.3005620","article-title":"Label-free porous silicon membrane waveguide for DNA sensing","volume":"93","author":"Rong","year":"2008","journal-title":"Appl. Phys. Lett."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1016\/j.bios.2008.01.017","article-title":"Nanoscale porous silicon waveguide for label-free DNA sensing","volume":"23","author":"Rong","year":"2008","journal-title":"Biosens. Bioelectron."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"24626","DOI":"10.1364\/OE.23.024626","article-title":"Spectrometer-free biological detection method using porous silicon microcavity devices","volume":"23","author":"Li","year":"2015","journal-title":"Opt. Express"},{"key":"ref_30","unstructured":"Wang, Y.K., and Huang, C.W. (2004, January 19). DNA microarray image analysis using active contour model. Proceedings of the IEEE Conference on Computational Systems Bioinformatics, Stanford, CA, USA."},{"key":"ref_31","unstructured":"Wang, Y., Shih, F.Y., and Ma, M.Q. (2005, January 21\u201326). Precise gridding of microarray images by detecting and correcting rotations in subarrays. Proceedings of the 8th Joint Conference on Information Sciences, Newark, CA, USA."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1109\/TNB.2010.2050900","article-title":"3-d spot modeling for automatic segmentation of cDNA microarray images","volume":"9","author":"Zacharia","year":"2010","journal-title":"IEEE Trans. Nanobiosci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1016\/S0031-3203(02)00170-X","article-title":"Robust adaptive spot segmentation of DNA microarray images","volume":"36","author":"Liew","year":"2003","journal-title":"Pattern Recognit."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1093\/bioinformatics\/bti455","article-title":"Segmentation of cDNA microarray spots using Markov radom field modeling","volume":"21","author":"Demirkaya","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/0031-3203(86)90030-0","article-title":"Minimum error threshold","volume":"19","author":"Kittler","year":"1986","journal-title":"Pattern C"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/S0167-8655(97)00059-7","article-title":"Minimum error thresholding: A note","volume":"18","author":"Jiulun","year":"1997","journal-title":"Pattern Recognit. Lett."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/0734-189X(85)90125-2","article-title":"A new method for gray-level picture thresholding using the entropy of the histogram","volume":"29","author":"Kapur","year":"1985","journal-title":"Comput. Vis. Graph. Image Process."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.cam.2006.07.019","article-title":"Toward a modified variational iteration method","volume":"207","author":"Abassy","year":"2007","journal-title":"J. Comput. Appl. Math."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1109\/TSMC.1979.4310076","article-title":"A threshold selection method from gray-level histograms","volume":"9","author":"Otsu","year":"1979","journal-title":"IEEE Trans. Syst. Man Cybern."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Burdescu, D.D., Brezovan, M., Ganea, E., and Stanescu, L. (2009). A New Method for Segmentation of Images Represented in a HSV Color Space, Springer.","DOI":"10.1007\/978-3-642-04697-1_57"},{"key":"ref_41","unstructured":"Brese, C.L., and Zou, J.J. (2006, January 11\u201314). Automatic Gridding of Rotated Microarray Images. Proceedings of the International Conference on Biomedical and Pharmaceutical Engineering, Singapore."},{"key":"ref_42","unstructured":"Bracewell, R.N. (2000). The Fourier Transform & Its Applications, WCB\/McGraw Hill."},{"key":"ref_43","first-page":"337","article-title":"A fast and novel skew estimation approach using radon transform","volume":"5","author":"Aithal","year":"2013","journal-title":"Int. J. Comput. Inf. Syst. Ind. Manag. Appl."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Antoniol, G., Ceccarelli, M., and Petrosino, A. (2005, January 14). Microarray image addressing based on the Radon transform. Proceedings of the IEEE Conference on Image Processing, Genova, Italy.","DOI":"10.1109\/ICIP.2005.1529675"},{"key":"ref_45","unstructured":"Deng, N., and Duan, H. (2005, January 17\u201318). An Automatic and Power Spectra-based Rotate Correcting Algorithm for Microarray Image. Proceedings of the 2015 IEEE Engineering in Medicine and Biology 27th Annual Conference, Shanghai, China."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Meyenhofer, F., Schaad, O., Descombes, P., and Kocher, M. (2007, January 22\u201326). Automatic analysis of microRNA Microarray images using Mathematical Morphology. Proceedings of the 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France.","DOI":"10.1109\/IEMBS.2007.4353780"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1016\/S0045-7949(01)00046-3","article-title":"Determination of the minimum bounding box of an arbitrary solid: An iterative approach","volume":"79","author":"Chan","year":"2001","journal-title":"Comput. Struct."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1016\/j.patcog.2006.08.003","article-title":"A simple method for fitting of bounding rectangle to closed regions","volume":"40","author":"Chaudhuria","year":"2007","journal-title":"Pattern Recognit."},{"key":"ref_49","first-page":"1382","article-title":"New algorithm for minimum enclosing rectangle of the object in the image region based on center-of-gravity principle","volume":"42","author":"Zhang","year":"2013","journal-title":"Infrared Laser Eng."},{"key":"ref_50","first-page":"1","article-title":"An overview of DNA microarray grid alignment and foreground separation approaches","volume":"1","author":"Bajcsy","year":"2006","journal-title":"EURASIP J. Adv. Signal Process."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Guirong, W., and Jian, S. (2009, January 24\u201326). Microarray Image Processing Using Expectation Maximization Algorithm and Mathematical Morphology. Proceedings of the IEEE Conference on CSO, Sanya, China.","DOI":"10.1109\/CSO.2009.91"},{"key":"ref_52","first-page":"520","article-title":"Robust protein microarray image segmentation using improved seeded region growing algorithm","volume":"1","author":"Wang","year":"2003","journal-title":"Chin. Opt. Lett."},{"key":"ref_53","unstructured":"Park, C.B., Lee, K.W., and Lee, S.W. (2004, January 26). Automatic Microarray Image Segmentation Based on Watershed Transformation. Proceedings of the IEEE Conference on Pattern Recognition, Cambridge, UK."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1007\/BF01934268","article-title":"Least-squares fitting of circles and ellipses","volume":"34","author":"Gander","year":"1994","journal-title":"BIT Numer. Math."}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/17\/6\/1335\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:38:26Z","timestamp":1760207906000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/17\/6\/1335"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,8]]},"references-count":54,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2017,6]]}},"alternative-id":["s17061335"],"URL":"https:\/\/doi.org\/10.3390\/s17061335","relation":{},"ISSN":["1424-8220"],"issn-type":[{"type":"electronic","value":"1424-8220"}],"subject":[],"published":{"date-parts":[[2017,6,8]]}}}