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Novel methods for microscopy and related analysis in systems biology research

Sharif Chowdhury’s doctoral dissertation examines the development and application of computational methods for the acquisition and analysis of images from single-cell assays.

In recent years, the analysis of cell images has become a powerful tool for biological measurements. Several methods have been developed for acquiring images of cells and intracellular organelles. Sharif Chowdhury’s doctoral dissertation examines the development and application of computational methods for the acquisition and analysis of images from single-cell assays.

In his dissertation, Chowdhury evaluates several methods for focusing microscopes and proposes a novel strategy for focusing in time-lapse microscopy. He is able to show that focus-drift is a dynamical system with a low level of randomness.

“These results go out to show that the focus-drift in time-lapse microscopy can be efficiently tracked by introducing a model of the drift in the focusing system,” Chowdhury points out.

Chowdhury also formulates a novel method, MAMLE, for segmenting individual cells from a dense cluster. The MAMLE method is evaluated with de novo data sets and benchmark data from known public databases. The accuracy of the MAMLE method is confirmed through an empirical evaluation.

“My study further contributes to the empirical evaluation of methods for the detection of subcellular organelles. I also exhibit a few applications for the findings as a method for imaging and analysis in systems biology research,” Chowdhury concludes.

Public defence of a doctoral dissertation on Friday, 13 May 2016

MSc Sharif Chowdhury’s doctoral dissertation in the field of Information Technology for Health and Biology entitled ‘Image Analysis Algorithms for Single-Cell Study in Systems Biology’ will be publicly examined at the Faculty of Computing and Electrical Engineering of Tampere University of Technology in Auditorium TB109 in the Tietotalo building (address: Korkeakoulunkatu 1, Tampere, Finland) at 12 noon on Friday, 13 May 2016.

The opponents will be Professor Heikki Kälviäinen (Monash University, Malaysia) and Senior Researcher Daniel Nicorici (Orion Pharma Oyj). Professor Olli Yli-Harja from the Department of Signal Processing at TUT will act as Chairman.

Sharif Chowdhury comes from Bangladesh and currently works at Wapice Oyj.

Further information: Sharif Chowdhury, +358 (0) 40 678 2860, firstname.lastname@student.tut.fi

News submitted by: Sanna Kähkönen
Keywords: science and research