# Welcome to CompuMAINE

The Computational Modeling, Analysis of Imagery and Numerical Experiments (CompuMAINE) lab is an image and signal processing, analysis, and modeling laboratory located at the University of Maine flagship campus. It was founded by Dr. Andre Khalil. CompuMAINE applies mathematical methods, particularly wavelet-based characterization, to images to elucidate and quantify novel properties of scientific interest. CompuMAINE is a proud partner of the Maine Cancer Foundation.

Projects range from multifractal image analysis to wavelet-based segmentation and characterization of chromosome territories and mammograms to the study of the interstellar medium. Over the years, we have adapted and further developed our methodologies for 1D, 2D, and 3D data analysis, in particular to perform a fractal-based segmentation of microcalcification clusters from breast tissue backgrounds of varying densities and to accurately segment objects of interest from fluorescence microscopy images with noisy backgrounds.

Take a look at CompuMAINE’s research and get to know our lab members. Let us know if you’re interested in working with us.

## News

2018 01 01: Dr. Khalil is now a member of the Department of Chemical and Biomedical Engineering at UMaine and will no longer be in Mathematics and Statistics.

2017 10 27: Undergrad lab member Dan D'Alessio received a $1,000 fellowship from the UMaine CUGR (Center for undergraduate research). Congratulations Dan!

2017 09 13: Another major lab milestone was achieved with the publication in the journal Methods of our manuscript Wavelet-based tracking of bacteria in unreconstructed off-axis holograms.

2017 09 01: The National Science Foundation's Major Research Instrumentation program awarded ~$500K towards the acquisition of a digital light sheet microscope Leica TCS SP8 DLS. Dr. Khalil is a co-PI on this project.

2017 05 14: Nice article by Lindsay Tice from the Sun Journal, on cutting-edge research being done right here in Maine, describing "10 of the most promising projects in Maine". One of these projects (at the end of the article) discusses our breast cancer research.

2017 04 30: Presentation of a poster on wavelet-based tracking of bacteria in unreconstructed off-axis holograms at the Maine Biological and Medical Sciences Symposium.

2017 04 30: High school lab member Clara Bradley accepted an offer to start her university studies in bioengineering at Stanford University. Congratulations Clara!.

2017 04 25: Through the University of Maine Faculty Research Funds program, Dr. Khalil was awarded a 2017 Summer Faculty Research Award for work on Wavelet Leaders vs. the Wavelet Transform Modulus Maxima Method.

2017 04 22: Dr. Khalil gave a short speech at the UMaine Marches for Science event. Here is a clip of the speech.

2017 04 21: Our paper Computational growth model of breast microcalcification clusters in simulated mammographic environments, published in Computers in Biology and Medicine, was given the **honors status**. Out of ~1,500 papers submitted to this journal in 2016, ~300 were accepted for publication, and amongst the top-ranked 80 out of the 300, ours was listed as "**meritorious**" and ranked as 38.

2017 04 01: Graduate student lab member Zach Marin accepted a PhD position in biomedical engineering at Yale University. Congratulations Zach!

2017 03 14: Through the NVIDIA GPU Grant Program, we were awarded a powerful Titan X Pascal graphics card to help accelerate our wavelet-transform calculations.

2017 03 14: A major lab milestone was achieved with the publication in Medical Physics of our manuscript "Mammographic evidence of microenvironment changes in tumorous breasts".

2017 03 11: Faculty lab member Rob Niemeyer accepted a position as assistant professor of mathematics at the University of the Incarnate Word, San Antonio, TX. Congratulations Rob!

2017 03 08: Some lab members are graduating / moving on to other projects. We're actively looking for new undergraduate and graduate students. Please visit the positions section.

## Positions

## Projects

## Publications

*Published Refereed Journal Articles*

- Marin, Z, Wallace, JK, Nadeau, J and Khalil, A 2017 Wavelet-based tracking of bacteria in unreconstructed off-axis holograms. Methods. https://doi.org/10.1016/j.ymeth.2017.09.003
- Marin, Z, Batchelder, KA, Toner, BC, Guimond, L, Gerasimova-Chechkina, E, Harrow, AR, Arneodo, A and Khalil, A 2017 Mammographic evidence of microenvironment changes in tumorous breasts. Medical Physics, 44, 1324-1336. doi:10.1002/mp.12120
- Gerasimova-Chechkina, E, Toner, B, Marin, Z, Audit, B, Roux, SG, Argoul, F, Khalil, A, Gileva, O, Naimark, O, Arneodo, A 2016 Comparative multifractal analysis of dynamic infrared thermograms and X-ray mammograms enlightens changes in the environment of malignant tumors, Frontiers in Physiology, 7, 336 (15 pages).
- Plourde, SM, Marin, Z, Smith, ZR, Toner, BC, Batchelder, KA, Khalil, A 2016. Computational growth model of breast microcalcification clusters in simulated mammographic environments. Computers in Biology and Medicine, 76, 7-13.
- Richard, CD, Tanenbaum, AB, Audit, B, Arneodo, A, Khalil, A, Frankel, WN 2015. SWDreader: A Wavelet-Based Algorithm Using Spectral Phase to Detect and Characterize Spike-Wave Discharges in Three Genetic Mouse Models of Absence Epilepsy, Journal of Neuroscience Methods, 242, 127.
- Batchelder, KA, Tanenbaum, AB, Albert, S, Guimond, L, Kestener, P, Arneodo, A, Khalil, A 2014. Wavelet-based 3D reconstruction of microcalcification clusters from two mammographic views: New Evidence that fractal tumors are malignant and Euclidean tumors are benign, PLoS One, DOI: 10.1371/journal.pone.0107580.
- Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Argoul, F, Naimark, O, Gileva, O, Arneodo, A 2014. Interdisciplinary approach for estimating and differentiating healthy and cancerous breast tissues with a multifractal analysis of skin temperature dynamics, Russian Journal of Biomechanics, 18(1), 90.
- Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Gileva, O, Argoul, F, Naimark, O, Arneodo, A 2014 Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis, Frontiers in Physiology, 5, 176.
- Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Argoul, F, Naimark, O, Arneodo, A, 2013. Multifractal Analysis of Dynamic Infrared Imaging of Breast Cancer, Europhysics Letters, 104 (6), 68001.
- Wu, Y, Batuski, D, Khalil, A, 2013. Nearest Neighbor Vector Analysis of SDSS DR5 Galaxy Distribution, Natural Science, 5 (1), 26619.
- Goody, MF, Kelly, MW, Reynolds, CJ, Khalil, A, Crawford, BD, Henry, CA 2012. NAD+ Biosynthesis Ameliorates a Zebrafish Model of Muscular Dystrophy, PLoS Biology, 10 (10), e1001409.
- Wu, Y, Batuski, D, Khalil, A, 2012. Three-Dimensional Filamentation Analysis of SDSS DR5 Survey, IRSN Astronomy & Astrophysics, 171829.
- McAteer, RT, Kestener, P, Arneodo, A, Khalil, A 2010. Automated Coronal Loop Detection using a Wavelet Transform Modulus Maxima Method, Solar Physics, Solar Image Processing and Analysis, 262,387-397.
- Robitaille, JF, Joncas, G, Khalil, A 2010. Morphological Analysis of HI Features. III. Metric Space Technique Revisited, Monthly Notices of the Royal Astronomical Society, 405, 636-656.
- Kestener, P, Conlon, PA, Khalil, A, Fennell, L, McAteer, RTJ, Gallagher, PT, Arneodo, A 2010. Characterising Complexity in Compound Systems: Segmentation in Wavelet-Space, Astrophysical Journal, 717, 995-1005.
- Goody, MF, Kelly, MW, Lessard, KN, Khalil, A, Henry, CA 2010. Nrk2b-mediated NAD+ production regulates cell adhesion and is required for muscle morphogenesis in vivo: Nrk2b and NAD+ in muscle morphogenesis, Developmental Biology, 344, 809-826.
- Grant, J, Verrill, C, Coustham, V, Arneodo, A, Paladino, F, Monier, K, Khalil, A 2010. Perinuclear distribution of heterochromatin in developing C. elegans embryos, Chromosome Research, 18, 873-885.
- Khalil A, Aponte, C, Zhang R, Davisson, TH, Dickey, I, Engelman D, Hawkins M, Mason, M 2009. Image analysis of soft-tissue in-growth and attachment into highly porous alumina ceramic foam metals, Medical Engineering and Physics, 31, 775-783.
- Wu, Y, Batuski, D, Khalil, A 2009. Multi-Scale Morphological Analysis of SDSS DR5 Survey Using the Metric Space Technique, Astrophysical Journal, 707, 1160-1167.
- Roland, T, Khalil, A, Tanenbaum, A, Berguiga, L, Delicheree, P, Bonneviot, L, Elezgaray, J, Arneodo, A, Argoul, F 2009. Revisiting the physical processes of vapodeposited thin gold films on chemically modified glass by atomic force and surface plasmon microscopies, Surface Science, 603, 3307-3320.
- Snow, CJ, Goody, M, Kelly, MW, Oster, EC, Jones, R, Khalil, A, and Henry, CA 2008, Time-lapse analysis and mathematical characterization elucidate novel mechanisms underlying muscle morphogenesis. PLoS Genetics, 4(10):e1000219 (18pp).
- Snow CJ, Peterson, M, Khalil, A, Henry C 2008. Muscle development is disrupted in zebrafish embryos deficient for Fibronectin, Developmental Dynamics, 237, 2542-2553.
- Khalil, A, Grant, JL, Caddle, LB, Atzema, E, Mills, KD, Arneodo, A 2007. Chromosome territories have a highly non-spherical morphology and non-random positioning. Chromosome Research, 15, 899-916.
- Caddle, LB, Grant, JL, van Hase, J, Denegre, J, Shirley, BJ, Bewersdorf, J, Cremer, C, Arneodo, A, Khalil, A, & Mills, KD 2007 Heterologous chromosome territory neighborhoods promote translocation susceptibility in primary lymphocytes. Chromosome Research, 15, 1061-1073.
- Khalil, A, Joncas, G, Nekka, F, Kestener, P, & Arneodo, A 2006, Morphological Analysis of HI Features II: Wavelet-Based Multifractal Formalism, Astrophysical Journal Supplement Series, 165, 512-550.
- Khalil, A, Joncas, G, & Nekka, F 2004, Morphological Analysis of HI Features I: Metric Space Technique, Astrophysical Journal, Vol. 601, 352-364

*Refereed Conference Articles*

- Gerasimova, E, Toner, B, Marin, Z, Audit, B, Roux, SG, Argoul, F, Khalil, A, Gileva, O, Naimark, O, Arneodo, A 2016 Combining multifractal analyses of digital mammograms and infrared thermograms to assist in early breast cancer diagnosis, in AIP Conference Proceedings, 1760, 020018 (11 pages).
- Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Gileva, O, Argoul, F, Naimark, O, Arneodo, A 2014 A wavelet-based method for multifractal analysis of medical signals: Application to dynamic infrared thermograms of breast cancer, in Nonlinear Dynamics of Electronic Systems: Communications in Computer and Information Science, 438, p. 288-300.
- Dickey, ID, Donahue, DW, Peshlov, B, Nohe, A, Khalil, A, Mason, M, Zhang, R, Aponte, C, Davisson, TH, Engelman, D, Hawkins, M 2009. Pore size modulates strength of soft-tissue in-growth and growth factor expression into novel porous titanium implants, Transactions of the Orthopaedic Research Society, 34, 2213.
- Khalil, A, Mason, M, Dickey, ID, Zhang, R, Aponte, C, Davisson, TH, Engelman, D, Hawkins, M 2009. Pore size and morphology modulate patterning of soft-tissue in-growth into porous titanium implants based on novel imaging tools, Transactions of the Orthopaedic Research Society, 34, 478.
- Khalil, A, Mason, M, Dickey, I, Zhang, R, Aponte, C, Davisson, T, Engelman, D, Hawkins, M 2008, Pattern of Soft Tissue In-Growth into Porous Implants Based on Novel Imaging Tools, Transactions of the Orthopaedic Research Society, 33, 1877.
- Mills, KD, Caddle, LB, Khalil, A, Bewersdorf, J. 2006. Imaging the Cancer Genome: High Resolution Microscopy and Quantitative Analyses, Optical Society of America, paper WB5, 3pp.
- Khalil A, Joncas G, Nekka F 2002. Exotic Tools for the Morphological Analysis of HI Clouds, ASP Conference Proceedings, Vol. 276, Edited by A. R. Taylor, T.L. Landecker, and A.G. Willis, San Francisco, Astronomical Society of the Pacific, p. 194-197.

*Published Conference Proceedings/Abstracts*

- Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG, Burgess, RW 2016. Dscam promotes self-avoidance in neurodevelopment by masking diverse cell adhesion molecules. Annual Meeting of the Society for Neuroscience: San Diego, CA.
- Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG, Burgess, RW 2015. Dscams promote selfavoidance by masking adhesion through both PDZ-dependent and –independent mechanisms. Annual Meeting of the Society for Neuroscience: Chicago, IL.
- Burgess, RW, Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG 2014. Dscams promote self-avoidance by masking adhesion through both MAGI-dependent and –independent mechanisms. Annual Meeting of the Society for Neuroscience: Washington, DC.
- Richard, CD, Khalil, A, Frankel, W 2013. Novel computational approach to detect absence seizures in mutant mouse strains. Annual Meeting of the Society for Neuroscience: San Diego, CA.
- Kestener, P, Khalil, A, Arneodo, A 2010. A continuous wavelet-based segmentation tool to analyze multifractal properties of quiet and active regions from solar magnetogram data. In ADA6, Astronomical Data Analysis Conference, Monastir, Tunisia.
- Wu, Y, Batuski, D, Khalil, A 2010. Properties of Density Field Clusters from the SDSS, Bulletin of the American Astronomical Society, 42, 385.
- Wu, Y, Batuski, D, Khalil, A 2009. Application of the Metric Space Technique in 2D and 3D to SDSS DR5, Bulletin of the American Astronomical Society, 41, 449.
- Wu, Y, Batuski, D, Khalil, A 2007. New statistical methods to analyze the Sloan Digital Sky Survey Data, Joint New England Sections of the American Physics Society and AAPT Spring Meeting.
- Wu, Y, Batuski, D, Khalil, A 2007. New Statistical Methods to Determine the Fractal Dimension of Structures Evident in the SDSS, WMAP, and 2MASS Surveys, Bulletin of the American Astronomical Society, 39, 804.
- Wu, Y, Batuski, D, & Khalil, A 2006. New statistical methods to analyze the SDSS DR5 galaxy distribution, Bulletin of the American Astronomical Society, 38, 1000.

*Theses*

- Marin, Zach 2017. Wavelet-Based Particle Tracking in Unreconstructed, Off-axis Holograms. MA Thesis. Mathematics. University of Maine.
- Toner, Brian 2015. The Geometric Properties of Cells Exhibiting Huntington’s Disease. MA Thesis. Mathematics. University of Maine.
- Ossana, Elliot 2015. Fractal Dimension of Residues Sets Within Pascal’s Triangle Under Square-Free Moduli. Honors Thesis. Mathematics. University of Maine.
- Plourde, Shayne 2015. Modeling the Growth of Breast Microcalcifications in Mathematically-Generated Breast Tissue Environments Using an AgentBased Model. Honors Thesis. Mathematics. University of Maine.
- Richard, Christian 2014. Novel Computational Approaches to Detect and Characterize Absence Seizures in Seizure-Prone Mutant Mouse Strains. PhD Thesis. Functional Genomics. University of Maine.
- Dewey, Hannah 2014. Wavelet-Based Multifractal Analysis of Brain Images. Honors Thesis. Mathematics. University of Maine.
- Cox, Derrick 2014. Computational Analysis of Mammographic Breast Tissue Using the Metric Space Technique. MA Thesis. Mathematics. University of Maine.
- Mooers, Kendra 2013. Characterization of Mammographic Breast Lesions And Their Microenvironment: An Application of a Wavelet-Based Multifractal Formalism. MA Thesis. Mathematics. University of Maine.
- Wu, Yongfeng 2010. Multi-Scale Three-Dimensional Analysis of Galaxy Distributions Using the Metric Space Technique. PhD Thesis. Astrophysics. University of Maine.
- Potter, Matthew 2010. Prime Modulo and Pascal’s Triangle As Seen With Fractal Geometry. MA Thesis. Mathematics. University of Maine.
- Grant, Jeremy 2008. Wavelet-Based Segmentation of Fluorescence Microscopy Images in Two and Three Dimensions. MA Thesis. Mathematics. University of Maine.
- Robitaille, Jean-Francois 2008. Analyse Metrique de Structure HI dans le Plan Galactique. MS Thesis. Astrophysics. Université Laval, QC, Canada.
- Wu, Yongfeng, 2007. New Statistical Methods to Get the Fractal Dimension of Bright Galaxies Distributions from the Sloan Digital Sky Survey Data. MS Thesis. Astrophysics. University of Maine.
- Khalil, Andre 2004. Structural Analysis of the Atomic Hydrogen in the Galactic Plane. PhD Thesis. Mathematics and Astrophysics. Universite Laval Quebec. 218pp.
- Khalil, Andre 1998. Exploration of the Fractal Dimension. MS Thesis. Mathematics. Concordia University Montreal. 68pp.

*Books*

- Wu, Y and Khalil, A 2009. The Evolution of the Universe. VDM Verlag, 76pp.
- Wu, Y, Batuski, D, and Khalil, A 2008. The Fractal Structure of the Universe. VDM Verlag, 80pp.

*Industry Reports*

- Khalil, A, Mason, MD 2008. Image Analysis of Soft-Tissue In-Growth into Artificial Bone Implants: Part II: PSF and SLM Implants, Stryker Orthopaedics, 4pp.
- Khalil, A, Mason, MD 2006. Image Analysis of Soft-Tissue In-Growth into and Attachment to Alumina Ceramic Foam for Canines, Stryker Orthopaedics, 14pp.

## Current Members

## Past Members

## Contact Details

425 Neville Hall

Department of Mathematics & Statistics

University of Maine

Orono, ME 04469-5752

Phone: (207) 581-3911

Email: compumaine@math.umaine.edu

### Acknowledgements

We would like to thank the Maine Cancer Foundation for all of their support.

Logo design by Shannon Meserve.