3 Years of my Life Spent Developing Image Processing Algorithms - Yours Free Open Source

Open Source Image Processing - Automated Analysis of Interfaces, Nano particles, Bubbles, and Electron Beam Effects in Liquid Cell Electron Microscopy

Our open source paper outlining the image processing algorithms we have developed over the last few years is live! The paper, code and sample videos are all available open source by the new Springer Open Journal Advanced Structural and Chemical ImagingWe maintain the code on GitHub, and have a screencast outlining the use of the algorithms on YouTube.

 

Automated analysis of evolving interfaces during in situ electron microscopy

Advanced Structural and Chemical Imaging 20162:2 DOI: 10.1186/s40679-016-0016-z
©  Schneider et al. 2016
Received: 15 November 2015
Accepted: 11 February 2016
Published: 26 February 2016

Abstract

In situ electron microscopy allows one to monitor dynamical processes at high spatial and temporal resolution. This produces large quantities of data, and hence automated image processing algorithms are needed to extract useful quantitative measures of the observed phenomena. In this work, we outline an image processing workflow for the analysis of evolving interfaces imaged during liquid cell electron microscopy. As examples, we show metal electrodeposition at electrode surfaces; beam-induced nanocrystal formation and dissolution; and beam-induced bubble nucleation, growth, and migration. These experiments are used to demonstrate a fully automated workflow for the extraction of, among other things, interface position, roughness, lateral wavelength, local normal velocity, and the projected area of the evolving phase as functions of time. The relevant algorithms have been implemented in Mathematica and are available online.

Comment

Nicholas M Schneider

Nicholas M Schneider is a 2010 graduate from the Kate Gleason College of Engineering who is now a Doctoral Candidate at the University of Pennsylvania. Originally from an obscure town south of Buffalo, New York, he attended the Rochester Institute of Technology where he received concurrent Bachelor of Science and Master of Science degrees. While there he had a number of Co-ops including a six month stay as a Design Engineer at Lockheed Martin and Research positions with Dr. Satish Kandlikar. Nicholas currently works with Dr. Haim H Bau in the field dubbed “in situ electron microscopy of liquid systems” where he studies applications in energy and biological systems. Outside of the lab, Nicholas Schneider is a Graduate Associate in Rodin College House and enjoys running (he ran his second Philly Marathon this past November), cooking, baking, reading, and justifying his coffee addiction by making it a hobby.

Penn Doctoral Defense - Liquid Cell Electron Microscopy with the nanoAquarium: Radiation and Electrochemistry

After five years at Penn, the time has come to defend my doctoral work. The experience  has been a journey of joy, growth, and discovery. I am both grateful and fortunate to have known and worked with so many wonderful people along the way.

The first half of the defense is a public presentation that will be open both physically and digitally. For those of you not able to make it in person, I will stream a live screencast to YouTube with the ability to comment and ask questions. If you can physically make the presentation, please see the details below. 

Nicholas M Schneider Doctoral Defense Details

Wednesday, 20 May 2015
University of Pennsylvania
Moore Building, Room 216 (Google Maps: http://bit.ly/1JqP4k4)
1:00 pm ET

Abstract

LIQUID CELL ELECTRON MICROSCOPY WITH THE NANOAQUARIUM: RADIATION AND ELECTROCHEMISTRY

Nicholas M Schneider

The advent of the electron microscope has fostered major advances in a broad spectrum of disciplines. The required vacuum environment of standard electron microscopy, however, precludes imaging of systems containing high vapor pressure liquids. The recent development of liquid cells like the Penn nanoaquarium overcomes this limitation, enabling imaging of temporally evolving processes in liquids with nanoscale resolution at video frame rates. We used Liquid Cell Electron Microscopy to investigate the morphological evolution of the electrode-electrolyte interface during electroplating, the onset of diffusive instabilities in electrodeposits, beam-mediated nucleation, growth, and dissolution of metallic nanoparticles, the nucleation and growth of nanobubbles, and the fundamentals of the electron-water interactions (Radiation Chemistry). The control of interfacial morphology in electrochemical processes is essential for applications ranging from nanomanufacturing to battery technologies. Critical questions still remain in understanding the transition between various growth regimes, particularly the onset of diffusion-limited growth. We present quantitative observations at previously unexplored length and time scales that clar- ify the evolution of the metal-electrolyte interface during deposition. The interface evolution during initial stages of galvanostatic Cu deposition on Pt from an acidic electrolyte is consistent with kinetic roughening theory, while at later times the behavior is consistent with diffusion limited growth physics. To control morphology, we demonstrate rapid pulse plating without entering the diffusion-limited regime, and study the effects of the inorganic additive Pb on the growth habit. The irradiating electrons used for imaging, however, affect the chemistry of the suspending medium. The electron beam’s interaction with the water solvent produces molecular and radical products such as hydrogen, oxygen, and hydrated (solvated) electrons. A detailed understanding of the interactions between the electrons and the irradiated medium is necessary to correctly interpret experiments, minimize artifacts, and take advantage of the irradiation as a tool. We predict the composition of water subjected to electron irradiation under conditions relevant to liquid cell electron microscopy. We interpret experimental data, such as beam-induced colloid aggregation and observations of crystallization and etching of metallic particles as functions of dose rate. Our predictive model is useful for designing experiments that minimize unwanted solution chemistry effects, extend liquid cell microscopy to new applications, take advantage of beam effects for nanomanufacturing such as the patterning of nanostructures, and properly interpreting experimental observations.

Comment

Nicholas M Schneider

Nicholas M Schneider is a 2010 graduate from the Kate Gleason College of Engineering who is now a Doctoral Candidate at the University of Pennsylvania. Originally from an obscure town south of Buffalo, New York, he attended the Rochester Institute of Technology where he received concurrent Bachelor of Science and Master of Science degrees. While there he had a number of Co-ops including a six month stay as a Design Engineer at Lockheed Martin and Research positions with Dr. Satish Kandlikar. Nicholas currently works with Dr. Haim H Bau in the field dubbed “in situ electron microscopy of liquid systems” where he studies applications in energy and biological systems. Outside of the lab, Nicholas Schneider is a Graduate Associate in Rodin College House and enjoys running (he ran his second Philly Marathon this past November), cooking, baking, reading, and justifying his coffee addiction by making it a hobby.

Upcoming Department Seminar: “In Situ Liquid Cell Electron Microscopy with the NanoAquarium: A Study in Electrochemistry and Radiation Chemistry”

Upcoming Department Seminar: “In Situ Liquid Cell Electron Microscopy with the NanoAquarium: A Study in Electrochemistry and Radiation Chemistry”

Nicholas M Schneider
Ph.D. Candidate, University of Pennsylvania 

“In Situ Liquid Cell Electron Microscopy with the NanoAquarium: A Study in Electrochemistry and Radiation Chemistry”
Advisor: Dr. Haim Bau

Abstract:
The advent of Electron Microscopy has fostered major advances in a broad spectrum of disciplines. The required vacuum of standard electron microscopy precludes imaging of process and objects suspended in liquid media. Many important processes, such as the potentially catastrophic formation of dendrites during battery cycling, take place in liquid systems. The recent development of liquid cells like the NanoAquarium overcomes this limitation, enabling imaging of temporally evolving processes in liquid systems with nanoscale resolution. I will describe the use of the NanoAquarium to investigate the morphological evolution of the electrode-electrolyte interface during electroplating and stripping of electrodes, nanoparticle growth and assembly, and the fundamentals of beam-irradiated medium interactions (Radiation Chemistry). The results of my work are applicable to battery technology and to nanomanufacturing.

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