Muhammad Farhan, Ph.D.

Program Director and Associate Professor, Electrical and Computer Engineering
Dhanani School of Science & Engineering


  • Ph.D. in Image Processing, Tampere University of Technology, Tampere, Finland
  • M.S. in Signal and Image Processing, Tampere University of Technology, Tampere, Finland
  • B.E. in Electronic Engineering, NED University of Engineering & Technology, Karachi, Pakistan

Awards & Honors

  • Rewarded with incentive by Tampere University of Technology for completion of Doctoral degree (research and course work (40 ECTS) both) in less than 3.5 years.
  • Research scholarship granted by NOKIA Foundation, Finland in 2012.
  • Received Tampere School of Science & Engineering (TISE) Graduate student travel grant for entire PhD.
  • 3rd position in poster competition at Summer School AMBIA, 2011.
  • HEC approved PhD supervisor.

Image Analysis for high-throughput, high-content screening studies for drug discovery.
(Collaboration of Tampere University of Technology, Finlad, and Biozentrum Basel, Switzerland).

Research Interests

  • Signal Processing
  • Image Processing
  • Pattern Recognition
  • Machine Learning
  • Statistical Signal Processing
  • Computer Vision
  • Biomedical Image Analysis
  • Biomedical Microscopy
  • Embedded Systems
  • Systems Biology

Courses Taught

  • Electric Network Analysis
  • Medical Image Processing (MS Course)
  • FPGA-based System Design
  • Microcontroller & Microprocessor systems
  • Integrated Circuits & Applications
  • Principles of Applied Mechatronics
  • Linear Circuit Analysis
  • Statistical Signal Processing (MS & Ph.D. course) at Tampere University of Technology, Finland during Spring 2013.


Dr. Muhammad Farhan has been involved in the field of Research and Academia for the past decade. It started from him joining SUPARCO, Pakistan in Jan. 2007 where he worked on Embedded Systems at Digital Systems Lab for around 2 years. During 2009-2014 he worked as Researcher and also as Lecturer in Department of Signal Processing, Tampere University of Technology, Tampere, Finland. From 2015 onwards, he has been involved in undergraduate engineering education in Pakistan with a mission of inculcating active R&D culture in the university as well as among students. He joined HU to carry on this mission and also to employ modern pedagogical methods focusing more on collaborative and engagement-based learning and instigating critical thinking, problem analysis and problem solving among students using active-learning approach.

Selected Publications

  •  M. Farhan, P. Ruusuvuori. M. Emmenlauer, P. Rämö, C. Dehio, and O. Yli-Harja, “Multi-scale Gaussian representation and outline-learning based cell image segmentation,”BMC Bioinformatics 2013, 14(Suppl 10):S6. Impact Factor: 2.435
  • S.S. Hassan, M. Farhan, R.Mangayil, H.Huttunen, and T.Aho, “Bioprocess data mining using regularized regression and random forests,”BMC Systems Biology 2013, 7(Suppl 1):S5. (corresponds to equal contribution and joint first author). Impact Factor: 3.15
  • M. Farhan, O. Yli-Harja, and A. Niemistö, “A novel method for splitting clumps of convex objects incorporating image intensity and using rectangular window-based concavity point-pair search,” Pattern Recognition Vol. 46, No. 3, pp. 741-751 (March 2013). Impact Factor: 3.4
  • M. Farhan, A. Larjo, O. Yli-Harja, and T.Aho, “Modeling bioprocess scale-up utilizing regularized linear and logistic regression,” to appear inProceedings of IEEE International Workshop on Machine Learning for Signal Processing, MLSP, Southampton, UK, 2013.
  • M. Farhan, P. Ruusuvuori, M. Emmenlauer, P. Rämö, O. Yli-Harja, and C. Dehio, “Graph cut and image intensity-based splitting improves nuclei segmentation in high-content screening,” in Proceedings of SPIE8655,Image Processing: Algorithms and Systems XI, 86550F,USA 2013.
  • M. Farhan, O. Yli-Harja, and A. Niemistö, “An improved clump splitting method for convex objects,” in Proceedings of the 7th International Workshop on Computational Systems Biology, Luxembourg, 2010, pp 35-38.
  • M. Farhan, “Image Analysis and Statistical Modeling for Applications in Cytometry and Bioprocess Control,” Doctoral Dissertation, Tampere University of Technology, Tampere, Finland, April 2014.
  • M. Farhan, “Automated clump splitting for biological cell segmentation in microscopy using image analysis,” Master of Science thesis, Department of Signal Processing, Tampere University of Technology, Tampere, Finland, October 2010.
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