@article {269, title = {Alignment of confocal scanning laser ophthalmoscopy photoreceptor images at different polarizations using complex phase relationships}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {56}, year = {2010}, abstract = {

A polarimetric technique for enhancing fundus images was recently introduced , where confocal scanning laser ophthalmoscopy (CSLO) images are acquired under differing incoming polarization states, and spatially resolved Mueller images are constructed based on the images. An important stage in this technique is the alignment of CSLO images acquired under differing polarization states. This has proven to be particularly difficult when dealing with photoreceptor images, which are characterized by poor SNRs and intensity inhomogeneities due to polarization properties. In this paper, an automated approach to aligning CSLO photoreceptor images acquired under differing polarization states is presented. A novel energy functional based on complex phase relationships is introduced that is invariant to polarization and scale, as well as robust to noise and highly sensitive to photoreceptor structural characteristics. A sequential quadratic programming approach is employed to determine the optimal alignment between the photoreceptor images by minimizing the proposed energy functional. The method has been tested on CSLO fish photoreceptor images acquired under differing polarization states and evaluated based on alignment accuracy. The results demonstrate that the proposed method outperforms existing techniques used for aligning CSLO images, with lower mean alignment error for all test cases.

}, keywords = {Algorithms, Animals, bio-optics, biomedical optical imaging, complex phase relationship, Computer-Assisted, Confocal, confocal scanning laser ophthalmoscopy, enhancing fundus image, eye, Fishes, Fundus Oculi, image enhancement, image processing, incoming polarization states, laser applications in medicine, light polarisation, medical image processing, Microscopy, Ophthalmoscopy, Photoreceptor Cells, photoreceptor image, polarimetry, Polarization, quadratic programming, sequential quadratic programming, spatially resolved Mueller image construction, Thermodynamics, Vertebrate}, issn = {0018-9294}, doi = {http://dx.doi.org/10.1109/TBME.2009.2017510}, author = {A Wong} } @inproceedings {349, title = {Watershed deconvolution for cell segmentation}, booktitle = {30th Annual Conference of the IEEE Engineering in Medicine and Biology Society}, year = {2008}, abstract = {

Cell segmentation and/or localization is the first stage of a (semi)automatic tracking system. We addressed the cell localization problem in our previous work where we characterized a typical blood stem cell in a microscopic image as an approximately circular object with dark interior and bright boundary. We also addressed the modelling of adjacent and dividing cells in our previous work as a deconvolution method to model individual blood stem cell as well as adjacent and dividing blood stem cells where an optimization algorithm was combined with a template matching method to segment cell regions and locate the cell centers. Our previous cell deconvolution method is capable of modelling different cell types with changes in the model parameters. However in cases where either a complex parameterized shape is needed to model a specific cell type, or in place of cell center localization, an exact cell segmentation is needed, this method will not be effective. In this paper we propose a method to achieve cell boundary segmentation. Considering cell segmentation as an inverse problem, we assume that cell centers are located in advance. Then, the cell segmentation will be solved by finding cell regions for optimal representation of cell centers while a template matching method is effectively employed to localize cell

}, keywords = {Algorithms, Artificial Intelligence, Automated, Cells, Computer-Assisted, Cultured, hematopoietic stem cells, Humans, image enhancement, image interpretation, Microscopy, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity}, doi = {http://dx.doi.org/10.1109/IEMBS.2008.4649168}, author = {N Nezamoddin Kachouie and P Fieguth and E Jervis} } @article {356, title = {Extended-Hungarian-JPDA: Exact single-frame stem cell tracking}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {54}, year = {2007}, pages = {2011 - 2019}, abstract = {

The fields of bioinformatics and biotechnology rely on the collection, processing and analysis of huge numbers of biocellular images, including cell features such as cell size, shape, and motility. Thus, cell tracking is of crucial importance in the study of cell behaviour and in drug and disease research. Such a multitarget tracking is essentially an assignment problem, NP-hard, with the solution normally found in practice in a reduced hypothesis space. In this paper we introduce a novel approach to find the exact association solution over time for single-frame scan-back stem cell tracking. Our proposed method employs a class of linear programming optimization methods known as the Hungarian method to find the optimal joint probabilistic data association for nonlinear dynamics and non-Gaussian measurements. The proposed method, an optimal joint probabilistic data association approach, has been successfully applied to track hematopoietic stem cells.

}, keywords = {Algorithms, Animals, biocellular images, bioinformatics, biological techniques, biotechnology, cell motility, cell shape, cell size, Cells, cellular biophysics, Computer-Assisted, Data Interpretation, extended-Hungarian-joint probabilistic data association, hematopoietic stem cells, Humans, image enhancement, image interpretation, linear programming optimization methods, Microscopy, multitarget tracking, nonGaussian measurements, nonlinear dynamics, optimal joint probabilistic data association, principal component analysis, Reproducibility of Results, Sensitivity and Specificity, single-frame scan-back stem cell tracking, Statistical, Video}, issn = {0018-9294}, doi = {http://dx.doi.org/10.1109/TBME.2007.895747}, author = {N Nezamoddin Kachouie and P Fieguth} }