Contact info:

  • Email: averma (at) mbl.edu

I am currently working at Marine Biological Lab in Woods Hole, MA after completing my M.S. in Biomedical Engineering from Drexel University, Philadelphia in 2009. At MBL, I work on developing state-of-the-art imaging systems, microscopy applications and techniques.

My research is in two broad categories:

  • Algorithm development, image processing, instrumentation, image/data analysis and signal processing. I also use MATLAB with Java and C# to develop customizable GUI based solutions.
  • Imaging assays/techniques for live imaging of chromosomes, neurons, embryos, cells, proteins, etc.
  • Research Gate Profile
  • Github Profile

Aside from my work, I enjoy traveling around the cape-bay area, music, movies, reading, sports, and of course, food!

short cv

Education:

  • MS Biomedical Engineering, Drexel University, 2009
  • B.Tech Biotechnology, Allahabad Agricultural Institute Deemed University, 2005

Experience:

    Current: (2009 - present)
  • Biomedical/Software Engineer, Marine Biological Lab, Woods Hole, MA
  • Manager for OpenPolScope Resource at MBL
  • Web Designer/Administrator for OpenPolScope
  • Web Designer/Administrator for Imaging @ MBL
    Past:
  • Research Associate, Freedom2, Inc. (now Nuvilex, Inc.), Cherry Hill, NJ, 2008-2008
  • Graduate Research Assistant, Drexel University, Philadelphia, PA, 2007-2009
  • Researcher, Central Institute of Fisheries Education, Mumbai, India, 2005-2006

Participations:

Conferences:

  • 2015 ImageJ User & Developer Conference
  • 2012 ImageJ User & Developer Conference
  • Paper presentation "Robust Object-Oriented Segmentation for High-Content Screening". (Proceedings of 2nd Workshop on Microscopic Image Analysis with Applications in Biology, Piscataway, NJ, USA (2007)

Honors:

  • Drexel Dean's Fellowship
 

publications (as author/co-author)

AM Saffer, TI Baskin, A Verma, T Stanislas, R Oldenbourg, VF Irish. Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition. The Plant Journal 116 (3), 855-870. November 2023

Felix Spira, Sara Cuylen-Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael Sixt and Daniel W Gerlich. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife Sciences 6:e30867. November 2017

Adib Keikhosravi, Yuming Liu, Cole Drifka, Kaitlin M. Woo, Amitabh Verma, Rudolf Oldenbourg and Kevin W. Eliceiri. Quantification of collagen organization in histopathology samples using liquid crystal based polarization microscopy. Biomedical Optics Express 8(9):4243. September 2017

Molly McQuilken, Maximilian S. Jentzsch, Amitabh Verma, Shalin B. Mehta, Rudolf Oldenbourgand Amy S. Gladfelter. Analysis of Septin Reorganization at Cytokinesis Using Polarized Fluorescence Microscopy. Frontiers in Cell and Developmental Biology 5:42. May 2017

Rachel Tkacz, Md Joynul Abedin, Phillip Sheath, Shalin B. Mehta, Amitabh Verma, Rudolf Oldenbourg, Mainak Majumder. Phase Transition and Liquid Crystalline Organization of Colloidal Graphene Oxide as a Function of pH. Particle and Particle Systems Characterization. March 2017

Shalin B. Mehta, Molly McQuilken, Patrick J. La Riviere, Patricia Occhipinti, Amitabh Verma, Rudolf Oldenbourg, Amy S. Gladfelter and Tomomi Tani. Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells. Proceedings of the National Academy of Sciences 113(42). September 2016

McQuilken, M., Mehta, S. B., Verma, A., Harris, G., Oldenbourg, R., and Gladfelter, A. S. Polarized Fluorescence Microscopy to Study Cytoskeleton Assembly and Organization in live cells. Current Protocols (2015). http://dx.doi.org/10.1002/0471143030

Shalin B. Mehta, Molly McQuilken, Patricia Occhipinti, Amitabh Verma, Rudolf Oldenbourg, Amy S. Gladfelter, Tomomi Tani. Dynamics of Polymeric Protein Assemblies in Live Cells Revealed by Fluorescence Polarization Imaging of Single Molecules, Biophysical Journal, Volume 108, Issue 2, 337a, 2015. http://dx.doi.org/10.1016/j.bpj.2014.11.1840

S. Abrahamsson, M. McQuilken, S. B. Mehta, A. Verma, J. Larsch, R. Ilic, R. Heintzmann, C. I. Bargmann, A. S. Gladfelter, R. Oldenbourg, MultiFocus Polarization Microscope (MF-PolScope) for 3D polarization imaging of up to 25 focal planes simultaneously, Optics Express, 2015. http://dx.doi.org/10.1364/OE.23.007734

Tkacz, Rachel; Oldenbourg, Rudolf; Mehta, Shalin; Miansarigavzan, Morteza; Verma, Amitabh and Majumder, Mainak. pH Dependent Isotropic to Nematic Phase Transitions in Graphene Oxide Dispersions Reveal Droplet Liquid Crystalline Phases. Chem. Commun. 2014. The Royal Society of Chemistry. http://dx.doi.org/10.1039/C4CC00970C

M. Tani, T. Tani, S. Mehta, A. Verma, R. Oldenbourg. Polarized light microscopy in reproductive and developmental biology. Molecular Reproduction and Development 2013. http://dx.doi.org/10.1002/mrd.22221

A.K. Verma, A.K. Pal, S.M. Manush, T. Das, R.S. Dalvi, P.P. Chandrachoodan, P.M. Ravi and S.K. Apte, Persistent sub-lethal chlorine exposure augments temperature induced immunosuppression in Cyprinus carpio advanced fingerlings, Fish & Shellfish Immunology 2007;22:547-555 (Elsevier Publication: http://dx.doi.org/10.1016/j.fsi.2006.08.001)

A.K. Verma, A.K. Pal, S.M. Manush, T. Das, R.S. Dalvi, P.P. Chandrachoodan, P.M. Ravi and S.K. Apte, Persistent sub-lethal chlorine exposure elicits the temperature induced stress responses in Cyprinus carpio early fingerlings, Pesticide Biochemistry and Physiology 2007;87:229237 (Elsevier Publication: http://dx.doi.org/10.1016/j.pestbp.2006.08.001)

publications (acknowledgements)

Colm P. Kelleher et al. ,Long-range repulsion between chromosomes in mammalian oocyte spindles. Science Advances Vol.10(39) September (2024) https://doi.org/10.1126/sciadv.adq7540

Henson, J. H., Yeterian, M., Weeks, R. M., Medrano, A. E., Brown, B. L., Geist, H. L., Pais, M. D., Oldenbourg, R. and Shuster, C. B. (2015). Arp2/3 Complex Inhibition Radically Alters Lamellipodial Actin Architecture, Suspended Cell Shape, and the Cell Spreading Process. Mol. Biol. Cell, 26(5):887-900. http://dx.doi.org/10.1091/mbc.E14-07-1244

Shalin B Mehta et.al. Polarized light imaging of birefringence and diattenuation at high resolution and high sensitivity. Journal of Optics 2013. - Acknowledgements for image acquisition and processing. http://dx.doi.org/10.1088/2040-8978/15/9/094007

S. Abrahamsson et.al. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nature Methods 2013. - Acknowledgements for data processing. http://dx.doi.org/10.1038/nmeth.2277

S. Mehta & R. Oldenbourg. Polarized light imaging of birefringence and diattenuation at high resolution and high sensitivity. Journal of Optics 2013. Special issue on High Resolution Optical Imaging. In Communication. - Acknowledgements for software development, image processing and algorithm development. http://dx.doi.org/10.1088/2040-8978/15/9/094007

M. Shribak. Complete polarization state generator with one variable retarder and its application for fast and sensitive measuring of two-dimensional birefringence distribution. Journal of the Optical Society of America A 2011. - Acknowledgements for software development. http://dx.doi.org/10.1364/JOSAA.28.000410

publications (conferences & proceedings)

S.B. Mehta, M. McQuilken, A. Verma, A. Gladfelter, R. Oldenbourg & T. Tani. Measurement of position and orientation of single molecules and their assemblies using real-time fluorescence polarization microscope. Focus on Microscopy Conference 2014.

S. Mehta, A. Verma, G. Harris. R. Oldenbourg, T Tani. Algorithms for Measuring Orientation of Single and Ensemble of Molecules with Real-Time Fluorescence Polarization Microscope. IEEE International Symposium on Biomedical Imaging 2013.

M. Shribak & A. Verma (Marine Biological Lab, Woods Hole). DIC microscopy with high speed switching shear directions and its applications. The American Society for Cell Biology 2009.

Verma A.K., Kriete A. Robust Object-Oriented Segmentation for High-Content Screening. Department of Biomedical Engineering, Science and Health Systems. Proceedings of 2nd Workshop on Microscopic Image Analysis with Applications in Biology, Piscataway, NJ, USA (2007)

Kriete & A. Ghosh & N. Yalamanchili & A.K. Verma & D. Miller (Drexel University) Quantum-dot based imaging assays to characterize and model signaling pathways. Focus On Microscopy Conference 2007

Masters thesis work on Automated and Robust Object Oriented Segmentation dealing with the computational aspects of image processing, High Throughput Screening and feature extraction from fluorescent image datasets using MATLAB and Definiens Developer Life. Drexel University Philadelphia, PA

Bachelors research dissertation work on Biochemical, Molecular and Immuno-Haematological Responses in Cyprinus carpio to Temperature and Chlorine, dealing with the toxicological/stress effect at the cellular and molecular level. (BARC, BRNS, DAE) at Central Institute of Fisheries Education Mumbai, India

research interests

My interests are focused towards bridging the gap between instrumentation, experiments, analysis and presentation. Be it using DIC methods to study microtubules or Polarized light microscopy to elucidate the uniquiness of graphine: Signal processing, image analysis, machine vision are some of the key components required for 2D and 3D object recognition, segmentation, detection and tracking.

Visualization of meaningful data combining different layers or objects is the culmination of this pipeline. Developing algorithms for cleaning, suppressing and highlighting information has become a key in The Age of Big Data.

  • Development of new state-of-the-art imaging tools
  • Algorithm development, image processing, instrumentation, image/data analysis and signal processing
  • Object Orientated Image Analysis
  • Visualization