Matthew B. Smith

Current Position

2017-present, Post-doc in Guillaume Salbreux's lab at Francis Crick Institute. London UK.

Developing an interface to neural networks for segmenting fluorescent microscopy images. Create a semi-automatic pipeline to analyze and segment cells in living tissues and colonies.

Previous Position

2013-2017, Post-doc in Ewa Paluch's lab at MRC-LMCB, UCL. London UK.

Implementing a 3D agent based model of the the actin cortex, an organelle responsible for cell shape change and motility. Developing software and algorithms for 3D segmentation of fluorescent microscopy images.

Education

• 2007-2012, Ph. D. Physics Lehigh University.
• 2004-2006, B.S. Physics, Summa Cum Laude. California State University Chico.
• 1997-2002, B.S. Mechanical Engineering, California State University Chico.

Achievements

• 2011 Attended the 61^st Lindau Nobel Laureate Meeting, Lindau Germany.
• 2008 Yoshida Travel Award (Department of Physics, Lehigh University)
• 2007-2009 GAAN Fellowship (Grant from the U.S. department of Education to Lehigh University Department of Physics) which required a teaching assignment.
• 2002-2004 Completed Peace Corps two year service in The Gambia, West Africa. teaching math and science to students grades 7-9.

Publications

• "Actin cortex architecture regulates cell surface tension." Chugh P, Clark AG, Smith MB, Cassani DAD, Dierkes K, Ragab A, Roux PP, Charras G, Salbreux G, Paluch EK. Nat Cell Biol. 2017
• "An active contour ImageJ plugin to monitor daughter cell size in 3D during cytokinesis." Smith MB, Chaigne A, Paluch EK. Methods Cell Biol. 2017
• "New single-molecule speckle microscopy reveals modification of the retrograde actin flow by focal adhesions at nanometer scales." Yamashiro S, Mizuno H, Smith MB, Ryan GL, Kiuchi T, Vavylonis D, Watanabe N. Mol Biol Cell. 2014
• "Distributed actin turnover in the lamellipodium and FRAP kinetics." Smith MB, Kiuchi T, Watanabe N, Vavylonis D. Biophys J. 2013
• "Interactive, Computer-Assisted Tracking of Speckle Trajectories in Fluorescence Microscopy: Application to Actin Polymerization and Membrane Fusion," Matthew B. Smith, Erdem Karatekin, Andrea Gohlke, Hiroaki Mizuno, Naoki Watanabe, and Dimitrios Vavylonis, Biophys J. 2011.
  
• "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours," M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, and D. Vavylonis, Cytoskeleton 2010.
  
• "Automated Actin Filament Segmentation, Tracking, and Tip Elongation Measurements based on Open Active Contour Models," H. Li, T. Shen, M. B. Smith, I. Fujiwara, D. Vavylonis, and X. Huang, In Proc. of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, 2009.

Open Source Software from Publications

• Speckle TrackerJ, for tracking point-like particles in 2D images.
  http://athena.physics.lehigh.edu/speckletrackerj
  https://github.com/odinsbane/speckletrackerj
• JFilament, for tracking filament structures in 2D and 3D images.
  http://athena.physics.lehigh.edu/jfilament
  https://github.com/odinsbane/jfilament
• Deforming Mesh, active contours program for segmenting volumes in 3D.
  http://www.ucl.ac.uk/lmcb/meshplugin
  https://github.com/PaluchLabUCL/DeformingMesh3D-plugin

Conferences

• "Molecules to Meshes: Generating Tension in an Actin Cortex." (talk, MB Smith, P Chugh, D Cassani, AG Clark, G Salbreux, EK Paluch) ASCB December 2015 San Diego, CA.
• "Tension Generation in an actin Cortex." (poster, MB Smith, P Chugh, D Cassani, AG Clark, G Salbreux, EK Paluch) Physics of Living Matter, Cambridge, September 2015.
• "Tension Generation in an actin Cortex." (poster, MB Smith, P Chugh, D Cassani, AG Clark, G Salbreux, EK Paluch ) Circle Meeting, AMOLF Amsterdam, April 2015.
• "Actomyosin cortex Mechanics and Cell Shape Control." (talk, Smith MB, Salbreux G, Paluch E.) Tissue Modelling Club, UCL July 2014.
• "Stabilizing Cytokinesis with Elasticity." (talk, Smith MB, Salbreux G, Paluch E.) Institute for the Physics of Living Systems Inauguration, UCL April 2014.
• "Actin cortex mechanics in animal cell morphogenesis." (poster, Matthew B. Smith, Guillaume Salbreux, and Ewa Paluch) Membrane Dynamics and Blebbing, Oxford University Mathematical Institute. September 2013.
• "Model of actin turnover and the role of slowly diffusing oligomers in the lamellipodium," (talk, Matthew B. Smith and Dimitrios Vavylonis) Biophysical Society Annual Meeting 2012, San Diego, CA.
• "Model of Actin Turnover in the Lamellipodium that Reconciles Prior Experiment Results," (poster, Matthew B. Smith, Naoki Watanabe, and Dimitrios Vavylonis) 2011 American Society for Cell Biology Annual Meeting, Denver, CO.
• "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours." (poster, M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, D. Vavylonis) 2010 American Society for Cell Biology Annual Meeting, Philadelphia, PA.
• "Turnover Dynamics of Diffuse Actin and Regulators at the Leading edge", (talk, Matthew B. Smith, Naoki Watanabe and Dimitrios Vavylonis) 2010 Biophysical Society Annual Meeting, San Francisco, CA.
• "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours." (poster, M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, D. Vavylonis) The Cellular Cytoskeleton workshop, Pingree Park, CO. 2010.
• "Actin Filament Segmentation and Tracking using Active Contours."(poster, M. B. Smith, D. Vavylonis, T. Shen, H. Li, X. Huang, M. Fedorka, A. Ruby, L. Vasko) 2009 Computational Science and Engineering/HPC Workshop, Lehigh University, Bethlehem, PA.
• "Mechanisms of large length fluctuations during actin filament growth." (poster Matthew B. Smith, Dimitrios Vavylonis) 2009 Biophysical Society Annual Meeting, Boston, MA.
• "Turnover dynamics of diffuse actin and regulators at the leading edge." (poster, Matthew B. Smith, Naoki Watanabe and Dimitrios Vavylonis) 2009 American Society for Cell Biology Annual Meeting, San Diego, CA.
• "Mechanisms of large length Fluctuations during actin Filament growth." (talk, Matthew B. Smith, Dimitrios Vavylonis) 2009 The American Physical Society March Meeting, Pittsburgh, PA.
• "The effect of cooperative polymerization kinetics in actin filament elongation rate and length fluctuations." (poster, M.B. Smith and D. Vavylonis) 2009 Lehigh University Research Symposium.