Automatic alignment and comparison of petri dish images containing cell colonies : submitted to the Institute of Information & Mathematical sciences in partial fulfillment of the requirements for the degree of Master of Information Science in Software Engineering at Massey University

Simple item page
dc.contributor.authorAlqahtani, Safar A
dc.date.accessioned2016-12-18T19:59:22Z
dc.date.available2016-12-18T19:59:22Z
dc.date.issued2016
dc.description.abstractThis work proposes a novel approach comprising of a chain of algorithms, for comparing, matching and aligning pairs of cell colony images taken at different stages on a Petri dish. The objective is to provide an assistive tool for microbiologists to quantify the loss or growth of cell colonies on two Petri dishes, by mapping cell colonies between a pair of images. This problem is highly non-trivial, as the shape, size and position of the corresponding colonies vary randomly. In addition, the cell colony images for comparison were taken at different times and from slightly different perspectives (i.e. effects of shearing); therefore, amplifying the complexity of the problem. Preliminary studies show that approaches purely based on SIFT or SURF, as well as algorithms used in astronomy, do not perform well on the problem domain. We therefore introduce a new approach to addressing these problems. A novel iterative technique that combines triangulation algorithms with the RANSAC alignment algorithm and AdaBoost classifer for alignment validation is proposed. Using 60 pairs of images of Petri dishes containing real biological cell colonies, we demonstrate the efficacy of the new algorithm in comparison to existing ones found in the literature. Empirical results show that the new proposed algorithm, we call K-NT for cell colonies matching, performed 4 times more accurate than other existing triangulation-based pattern matching algorithms. In the last stage of processing, we were able to generate an AdaBoost classifer with an accuracy of 98.5% that helps validate if an image was successfully aligned or not.en_US
dc.identifier.urihttp://hdl.handle.net/10179/10157
dc.language.isoenen_US
dc.publisherMassey Universityen_US
dc.rightsThe Authoren_US
dc.titleAutomatic alignment and comparison of petri dish images containing cell colonies : submitted to the Institute of Information & Mathematical sciences in partial fulfillment of the requirements for the degree of Master of Information Science in Software Engineering at Massey Universityen_US
dc.typeThesisen_US
massey.contributor.authorAlqahtani, Safar Aen_US
thesis.degree.disciplineSoftware Engineeringen_US
thesis.degree.grantorMassey Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Information Science (M.Inf.Sc.)en_US
Files
Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
01_front.pdf
Size:
112.48 KB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
02_whole.pdf
Size:
15.48 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
3.32 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Theses and Dissertations