Scientific Imaging

Image Processing and Computer Vision are very broad concepts, applicable to any number of contexts involving data acquisition from a camera of some sort.  Most images studied in the context of denoising or compression are every-day, human-world images, photos of people, buildings, scenery etc.  The human world has a complex structure, full of straight lines and edges, and is difficult to model, therefore many of the methods developed for such images are heuristic in nature.

In contrast, scientific imaging refers to working on two- or three-dimensional imagery taken for a scientific purpose, in most cases acquired either through a microscope or remotely-sensed images taken at a distance.  In contrast to the complex structure of the human (meter) scale, at both the micron scale (crystals, grains of sand, groups of cells) and at the kilometer scale (forests, deserts) the natural world has a much more random, textured, or irregular structure which can often well be modeled mathematically as a random field.

The methods developed for scientific imaging tend to be less heuristic, and more model based, than those in photographic image processing.  Markov random fields, Gibbs random fields, hidden Markov models, and wavelet models are some of the approaches which we use here.

Related people


 Alexander Wong, David A. Clausi, Paul Fieguth


Farnoud Kazemzadeh, Shahid Haider, Ruben Yousuf, Jason Deglint, Hicham Sekkati


Azadeh Mohebi, Simon Alexander, Sunil Sinha, Wesley Campaigne, Ying Liu, Justin Eichel, Zohreh Azimifar

Related demos

Porous Media
Multiplexed Optical High-coherence Interferometry

 Related publications

 Journal articles

Haider, S.A. CameronP. SivaD. LuiM. J. ShafieeA. Boroomand, N. Haider, and A. Wong, "Fluorescence microscopy image noise reduction using a stochastically-connected random field model", Nature Scientific Reports, Submitted. Details

Boroomand, A.A. Wong, E. Li, D. Cho, B. Ni, and K. Bizheva, "Multi-penalty conditional random field approach to super-resolved reconstruction of optical coherence tomography images", Biomedical Optics Express, Accepted.Details

Li, F.L. XuA. Wong, and D. A. Clausi, "Feature Extraction for Hyperspectral Imagery via Ensemble Localized Manifold Learningpdf", IEEE Geoscience and Remote Sensing Letters, vol. 12, issue 12, 2015. Details

Kazemzadeh, F.S. HaiderC. ScharfenbergerA. Wong, and D. A. Clausi, "Multispectral Stereoscopic Imaging Device: Simultaneous Multiview Imaging from the Visible to the Near-Infraredpdf", IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT, vol. 63, issue 7: IEEE Instrumentation and Measurement Society, pp. 1871-1873, July 2014. Details

Wong, A.J. GlaisterA. Cameron, and M. A. Haider, "Correlated Diffusion Imaging", BMC Medical Imaging, 2013.Details

Campaigne, W., and P. Fieguth, "Frozen State Hierarchical Annealingpdf", IEEE Transactions on Image Processing, vol. 22, no. 4, pp. 1486-1497, 2013. Details

Moayed, A. A., S. Hariri, C. LiuA. Wong, V. Choh, and K. Bizheva, "Stimulus Specific Pupil Dynamics Measured In-vivo in Birds (Gallus Gallus Domesticus) with Ultrahigh Resolution Optical Coherence Tomography", Investigative Ophthalmology and Visual Science, 11, vol. 53, issue 6869, 2012. Details


Mohebi, A.P. Fieguth, and M. A. Ioannidis, "Statistical fusion of two-scale images of porous mediapdf", Advances in Water Resources, vol. 32, no. 11, pp. 1567 - 1579, 2009. Details

Ioannidis, M. A., S. K. AlexanderP. Fieguth, and E. Vrscay, "Hierarchical annealing for synthesis of binary imagespdf",Mathematical Geosciences, vol. 41: Springer Berlin / Heidelberg, pp. 357-378, 2009. Details

Sinha, S. K., and P. Fieguth, "Automated detection of crack defects in buried concrete pipe imagespdf", Automation in Construction, vol. 15, no. 1, pp. 58 - 72, 2006. Details

Sinha, S. K., and P. Fieguth, "Neuro-fuzzy network for the classification of buried pipe defectspdf", Automation in Construction, vol. 15, no. 1, pp. 73 - 83, 2006. Details

Sinha, S. K., and P. Fieguth, "Segmentation of buried concrete pipe imagespdf", Automation in Construction, vol. 15, pp. 47 - 57, 2006. Details

Sinha, S. K., and P. Fieguth, "Morphological segmentation and classification of underground pipe imagespdf", Machine Vision and Applications, vol. 17, pp. 21-31, 2006. Details

Sinha, S. K.P. Fieguth, and M. A. Polak, "Computer vision techniques for automatic structural assessment of underground pipespdf", Computer-Aided Civil and Infrastructure Engineering, vol. 18, no. 2: Blackwell Publishing Inc, pp. 95–112, 2003. Details

Fieguth, P., and D. H. Staelin, "High-accuracy profiler that uses depth from focuspdf", Applied Optics, vol. 33, no. 4: OSA, pp. 686 - 689, 1994. Details

Kazemzadeh, F.A. Wong, B. B. Behr, and A. R. Hajian, "Depth Profilometry via Multiplexed Optical High-Coherence Interferometry", PLoS ONE: PLoS. Details

Conference papers

Deglint, J.F. KazemzadehA. Wong, and D. A. Clausi, "Inference of dense spectral reflectance images from sparse reflectance measurement using non-linear regression modeling", SPIE Optics and Photonics, Applications of Digital Image Processing XXXVIII, August, 2015. Details
Haider, S.D. ChoR. AmelardA. Wong, and D. A. Clausi, "Enhanced classification of malignant melanoma lesions via the integration of physiological features from dermatological photographspdf", 36th Annual International IEEE Engineering in Medicine and Biology Society Conference, Sheraton Chicago Hotel and Towers Chicago, IL, USA, pp. 6455-6458, September, 2014. Details

Kazemzadeh, F.S. HaiderA. WongC. Scharfenberger, and D. A. Clausi, "Concurrent Multiview Discrete Spectral Imaging Device from the VIS to the NIR", SPIE: Optics + Photonics, Novel Optical Systems Design and Optimization XVII , vol. 9193, San Diego, USA, SPIE Proceedings, 2014. Details

Kazemzadeh, F.M. J. Shafiee, A. Wong, and D. A. Clausi, "Reconstruction of Compressive Multispectral Sensing Data Using a Multi-layered Conditional Random Field Approach", SPIE: Optics + Photonics, vol. 9217, San diego, USA, SPIE Proceedings, 2014. Details
Schwartz, S.A. Wong, and D. A. Clausi, "Saliency-guided compressive fluorescence microscopy", 34th Annual International Conference of the IEEE Engineering in Medicine and Biology, , San Diego, USA., pp. 4365 - 4368 , 2012. Details

Mohebi, A.Y. Liu, and P. Fieguth, "Hierarchical sampling with constraintspdf", 6th International Conference on Image Analysis and Recognition, pp. 23 - 32, 2009. Details

Liu, Y., and P. Fieguth, "Image resolution enhancement with hierarchical hidden fieldspdf", 6th International Conference on Image Analysis and Recognition, pp. 73 - 82, 2009. Details

Liu, Y., and P. Fieguth, "Parallel hidden hierarchical fields for multi-scale reconstructionpdf", 7th International Conference on Energy Minimization Methods in Computer Vision and Pattern Recognition, pp. 70–83, 2009. Details

Mohebi, A., and P. Fieguth, "Modeling and reconstruction of two-scale porous media using MRI measurement", Fourth Biot Conference on Poromechanics, New York, 2009. Details

LLiu, Y.A. Mohebi, and P. Fieguth, "Modeling of multiscale porous media using multiple Markov random fields", Fourth Biot Conference on Poromechanics, New York, 2009. Details

Mohebi, A., and P. Fieguth, "Statistical fusion and sampling of scientific imagespdf", 15th IEEE International Conference on Image Processing, pp. 1312 - 1315, 2008. Details
 Mohebi, A., and P. Fieguth, "Posterior sampling of scientific imagespdf", 2006 International Conference on Image Analysis and Recognition, Portugal, Springer, 2006. Details

Alexander, S. K.P. Fieguth, and E. Vrscay, "Discrete-state modeling of porous media over multiple scales", SIAM Conference on Mathematical and Computational Issues in the Geosciences, Avignon, 2005. Details

Alexander, S. K.P. Fieguth, and E. Vrscay, "Hierarchical annealing of porous media", SIAM Conference on Mathematical and Computational Issues in the Geosciences, Avignon, 2005. Details

Fieguth, P., and S. K. Alexander, "Parameterized hierarchical annealing for scientific modelspdf", 2004 International Conference on Image Analysis and Recognition, Portugal, 2004. Details

Alexander, S. K.P. Fieguth, and E. Vrscay, "Hierarchical annealing for scientific modelspdf", 37th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Montreal, 2004. Details


Sinha, S. K., and P. Fieguth, "Assessment, rehabilitation and maintenance of buried pipes", International Pipeline Conference, San Diego, California, pp. 53 - 58, 2002. Details

Sinha, S. K., and P. Fieguth, "Development of an automated pipeline inspection system", International Conference on Underground Infrastructure Research, Waterloo, 2001. Details

Polak, M. A., S. K. Sinha, and P. Fieguth, "Development of an intelligent system for municipal infrastructure management", Canadian Society of Civil Engineering Conference, London, 2000. Details


Sinha, S. K., and P. Fieguth, "Detection of minor cracks on noisy buried sewer pipe images", VI Construction Conference, Orlando, 2000. Details

Karray, F., S. K. Sinha, and P. Fieguth, "Automated segmentation of underground pipe scanned images", World Automation Congress 2000, Hawaii, pp. 161 - 171, 2000. Details

McKim, R., S. K. Sinha, and P. Fieguth, "Novel system for automatic underground pipe distress detection and classification", Canadian Society of Civil Engineering Conference, Saskatchewan, pp. 279 - 288, 1999. Details

Sinha, S. K., F. Karray, and P. Fieguth, "Underground pipe cracks classification using image analysis and neuro-fuzzy algorithmpdf", IEEE Symposium on Intelligent Control, pp. 399 - 404, 1999. Details

Fieguth, P., and S. K. Sinha, "Automated analysis and detection of cracks in underground scanned pipespdf",International Conference on Image Processing, vol. 4, 1999. Details

McKim, R., S. K. Sinha, and P. Fieguth, "Automated underground sewage pipe condition assessment by image analysis of the state-of-the-art sewer scanner and evaluation technology surveyspdf", No Dig '99 International Conference, Orlando, 1999. Details


Fieguth, P., "Statistical Image Processing and Multidimensional Modeling", Information Science and Statistics: Springer, 2010. Details


Kazemzadeh, F., and A. Wong, A System, Method and Apparatus for Ultra-resolved Ultra-wide Field-of-view Multispectral and Hyperspectral Holographic Microscopy, vol. 62155416, USA, April 30, 2015. Details

Kazemzadeh, F., A. Wong, and S. Haider, Imaging System and Method for Concurrent Multiview Multispectral Polarimetric Light-field High Dynamic Range Imaging, USA, 2014. Details

Hajian, A. R., F. Kazemzadeh, B. B. Behr, T. M. Haylock, and L. M. Chifman, A Device and Methods for Generating a Fringe Pattern Based on the Depth of a Surface of a Substance, USA, 2011. Details


Eichel, J. A.Statistical Model-Based Corneal Reconstruction, , Waterloo, ON, Canada, University of Waterloo, 2013. Details

Campaigne, W., "Frozen-State Hierarchical Annealingpdf", Department of Systems Design Engineering, 2012. Details

Kazemzadeh, F., "Laser Interference Fringe Tomography - A Novel 3D Imaging Microscopy Techniquepdf", Department of Systems Design Engineering, Waterloo, University of Waterloo, 2011. Details

Fieguth, P., "Application of Multiscale Estimation to Large Multidimensional Imaging and Remote Sensing Problemspdf",Department of Electrical Engineering and Computer Science, Cambridge, Massachusetts, Massachusetts Institute of Technology, 1995.  Details