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Ali Zifan

zifan-ali.jpegDr Zifan holds the position of Assistant Adjunct Professor of Medicine IV in the Division of Gastroenterology at the University of California, San Diego (UCSD). He earned a BSc in Electrical Engineering in 2002, a MSc in Medical Engineering in 2006, MPhil in Information Engineering in 2008 and a PhD in Information Engineering in 2011 at City, University of London. He subsequently carried out 2 post-doctoral fellowships in Bioinformatics, and Gastroenterology at UC San Diego.

Personal Quotes

Until that last gasp of earthly air lights up the chandelier of my Lungs...Before that last rush of blood shakes the chambers of my Heart...

i will be seeking you, not in the confined realm of physical reality, but in the infinite realm of my dreams and the black holes of my imagination...

I would never search for perfection for I find so much beauty in the individuality and humanity of flaws and perceived imperfections, also known as character and uniqueness to the more optimistic types....

If the spiritual journey of life is the mending/fusion of the human Soul With bits and pieces of other mortals in order to reach Nirvana, may the Patches that you encounter on the shelves of the pricey shopping center of life, Be not the ones that you have to Long for, but those who aside from being A compatible match, are Worthy of the pleasure of your company...

Love' is that spark of magic light, which illuminates the road for the Train of Life through the crushing darkness of existence… It is solely your choice to provide the flame to guide the train of life to the right track, or gaze upon with despair the inevitable wrecked wreckage of an injudicious sealed fate, where hopes & aspirations seize to exist; mere murmurs & whispers in the wind…

Humility, don't you dare smother my Ego! don't you know that its divine and Godly?! Same goes to you Ego, may i remind you that you were created among other pious beings…As for Me: "I no longer desire to be your Balancing act…i want to be set free"

I live in the solitude which i found extremely painful when i was younger, but has become more delicious as i've matured....seems the solitude of a quite life stimulates the creative mind and inclines the original & powerful minded towards the Religion of Solitude

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PhD in Information Engineering (Computer Vision/Machine Learning), City University (London, United Kingdom). Awarded 2011.


MPhil in Information Engineering (Computer Vision/Machine learning), City University (London, United Kingdom).


MSc in Biomedical Engineering (Bio-electrics), Amir Kabir University of Technology (Tehran, Iran) Awarded 2006.


BSc in Electrical Engineering (Electronics), University of Indonesia (Jakarta, Indonesia). Awarded 2002.



“Integration of Geometric and Finite Element Modeling of the Thorax for Electrical Impedance Tomography (EIT) Lung Imaging,” PhD Thesis. Supervised by Professor Panos Liatsis, City University, London, United Kingdom.

“Blind Source Separation of Image Mixtures using Modified Independent Component Analysis”, MSc Thesis. Supervised by Dr. S.A. Salehi and Prof. M.H. Moradi, Department of Biomedical Engineering, Amir Kabir University of Technology, Tehran, Iran.



Selected Peer Reviewed Papers

  • Ali Zifan, Panos Liatsis, Brian E. Chapman, ‘ The use of the Kalman Filter in the automated segmentation of EIT lung images,’ Physiological Measurements, Vol. 34, pp-671-694, 2013
  • A. Zifan, M. H. Moradi, S. Gharibzadeh, ‘ Microarray Image Enhancement by Denoising using Decimated and Undecimated Multiwavelet Transforms,’ Signal, Image and Video Processing, 1863-1703, 2009
  • A. Andriotis,   A. Zifan, M. Gavaises, P. Liatsis, J. Pantos, A. Theodorakakos, E. Efstathopoulos, and D. Katritsis. ‘ A New Method of Three-dimensional Coronary Artery Reconstruction from X-ray Angiography: Validation against a Virtual Phantom and Multi-slice Computed Tomography,’ Catheterization and Cardiovascular Interventions, Vol.71, pp. 28-43, 2008.
  • A. Zifan, P. Liatsis P., P. Kantartzis, M. Gavaises M., N. Karcanias, and D. Katritsis, ‘ Automatic 3D Reconstruction of Coronary Arteries Centreline from Monoplane X-ray Angiogram Images,’ Int. J of Biological and Medical Sciences, Vol. 1, No 1, pp. 44-49, 2008.
  • A. Theodorakakos, M. Gavaises, A. Andriotis A,   A. Zifan, P. Liatsis, Pantos I, E. P. Efstathopoulos, D. Katritsis, ‘ Simulation of Cardiac Motion on Non-Newtonian, Pulsating Flow Development in the Human Left Anterior Descending Coronary Artery,’ Physics in Medicine and Biology 53:4875-4892, 2008.
  • A. Zifan, S. Gharibzadeh, M. Moradi, ‘ Could Dynamic Attractors Explain Associative Prosopagnosia?  ,’Medical Hypotheses, Volume 68, Issue 6, Pages 1399-1405, 2007.
  • A. Zifan, S. Gharibzadeh, ‘ The Chaotic Nature of Temper in Humans: A Long Short-term Memory Recurrent Neural Network Model,’ Medical Hypotheses, Volume 67, Issue 3, Pages 658-661, 2006.
  • A. Zifan, S. Saberi, M. H. Moradi, and F. Towhidkhah, ‘ Automated ECG Segmentation Using Piecewise Derivative Dynamic Time Warping’, Int. Journal of Biomedical Sciences, 1(3), 2006.

Competitive Research Grants Held

2013, NIH R01 4/1/20113/31/2017

Ischemia of Esophageal Wall – a Mechanism of Esophageal Pain
Goal of this study is to determine if ischemia of esophageal wall is the cause of esophageal pain. These studies will be conducted in healthy normal subjects and patients with esophageal pain using laser Doppler perfusion technique to determine the temporal correlation between symptoms and esophageal wall blood ischemia. Furthermore, we will determine if longitudinal muscle contraction of the esophageal wall causes reduction in esophageal wall blood flow. We will also explore the temporal correlation between esophageal symptoms and longitudinal muscle contraction of the esophagus using ambulatory high resolution manometry

2008-2011, Engineering and Physical Sciences Research Council (EPSRC), Grant EP/E029868/1, UK

Research grant for investigating “ A Novel Analogue Bio-impedance System-on-a-chip for Monitoring of Neonate Lung Function”.

Role: co-PI

The goal was to develop the component parts for a vitally needed integrated bio-imaging system for use to monitor lung function of neonates and children in ITUs. This novel system is based on the application of Electrical impedance Tomography (EIT) as an imaging modality, which remains the only viable solution for this application. Throughout the lifetime of the project considerable interest in the use of EIT for lung imaging has grown amongst clinicians, and members of this group have contributed to an international collaboration to standardize on a developmental algorithm for lung imaging. One of the papers produced from this research achieved the Martin Black award for best paper 2009 from the Institute for Physics Engineering and Medicine (IPEM).

2007-2008, The Heart Centre Ltd., Athens Euroclinic, Greece

Role: co-PI

Research grant for producing “ A new Software for the 3D reconstruction of Coronary Vessel Lumen from Monoplane Angiogram Images”.

The goal was to develop state-of-the-art software in Matlab/C++ for the 3D Reconstruction of Coronary vessels from 2D Angiogram images. Two such software were developed in the latter project.

Professional Development

Course Modules:


Designed the ‘Pattern Recognition’ Course Module (i.e., Slides, Booklet, Lab Assignments, Homework) for the graduate program at City University, London. It was designed in such a way to help students gain pattern recognition skills essentials in order to identify, understand, analyze and interpret images, along with the practical experience of trying out pattern recognition techniques in a MATLAB environment.


Designed the ‘Soft-Field Imaging Course Module (i.e., Slides, Booklet, Lab Assignments, Homework) for the graduate program at City University, London. The module provides a solid foundation to understand the technical content, and open problems of Soft-field Imaging, Methods to provide and to prepare a student for research and development in various aspects of Soft-field imaging. The module provides an up-to-date review of the history of the development of soft-field imaging techniques, the present state of knowledge, and an overview of future developments and applications.



Gullet X 1.0

The use of Intraluminal Esophageal Impedance for assessing dysphagia and LES lift.

Heartburn symptom analyzer.


3DCAR (Three-dimensional Coronary Artery Vessel Lumen Reconstruction):

3DCAR is a state-of-the-art interactive software in Matlab for the three dimensional visualization of the Arterial vessels from 2D Angiogram images. The software has the following features and outputs:

  • Automatic centerline extraction
  • Automatic sub-pixel edge extraction
  • 3D Vessel lumen reconstruction
  • Mesh export for computational fluid dynamic (CFD) processing and finite element analysis (FEA).

Tomographic Image Segmentation (TIS):

The GUI allows calculation of,

  • Forward mesh modeling: finite element model generation
  • Inverse Modeling: Regularized Tikhonov Reconstruction
  • Bayesian Spatio-temporal Segmentation
  • Wavelet based Segmentation
  • HMM segmentation


ICACE (Interactive Coronary Artery Centerline Extractor):

ICACE allows,

  • Non-linear PDE Denoising of X-ray Angiogram images
  • Multiscale vessel enhancement
  • Quantile based hysteresis thresholding
  • Skeletonization
  • Arterial tree extraction

Research Interests

  • Signal and Image Processing
  • Machine Learning
  • Pattern Recognition
  • Electrical Impedance Tomography
  • Image and Video Coding
  • Evolutionary Optimization
  • Artificial Neural Networks

Computer Skills

Matlab, C++, Python, ITK, VTK, Rhino3D, CUBIT, NETGEN, TetGen, MeshLab Windows, MS Office, Word, PowerPoint, Internet, Excel


  • Farsi, native speaker
  • English, fluent
  • Spanish, fluent
  • Bahasa Indonesia, very good