You are invited to the New England Society for Microscopy's Virtual Spring Symposium and Workshops! The meeting will take place on May 20th via Zoom, consisting of four technical talks, four lightning talks, and a demonstration of how to use Napari-Micromanager for microscope control.
Please register for the Symposium (for FREE!) to receive the Zoom link. Log on at 8:45 am, Symposium will begin at 9 am.
Symposium Schedule, May 7th
8:45 AM – Zoom Meeting will open for Symposium
9:00 AM –Welcome by NESM President
9:10 AM –Sara Hashmi (Northeastern University)
Using optical microscopy to measure droplet and colloidal particle mechanics in confined flows
9:50 AM – Tom Kirchhausen (HMS/Boston Childrens Hospital)
Using lattice light sheet microscopy to study membrane dynamics
10:30 AM – Coffee Break: Option of breakout rooms for chatting
10:50 AM - Igor Sokolov (Tufts University)
Novel multidimensional imaging with atomic force microscopy (AFM) and machine learning image processing are key for the first use of AFM in medicine
11:30 AM - Xingbo Yang (Harvard University)
A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging
12:10 PM - Break for lunch
1:00 PM - Lightning talks
1:00 PM - John Russell (Harvard University)
1:10 PM- Philip Seifert (Schepens Eye Research Institute- Massachusetts Eye and Ear)
1:20 PM - Robert Brandon (Bruker)
Topic: micro-XRF
1:30 PM - Rick Passey (ThermoFisher)
Topic: DualBeam FIB
1:40 PM - Elizabeth May (Harvard University)
1:50 PM – Coffee Break: Option of breakout rooms for chatting
Demonstration
2:00 PM - 3:00 PM - Ian Hunt-Isaak (Harvard University)
Demonstration of Napari-Micromanager
Napari-micromanager is a rapidly developing project providing Python-based, free and open-source software for operating light microscopes. It uses the core functionality from the Micromanager project but replaces the Java based user interface with one embedded in Napari - a high performance image viewer. This design allows for seamless interoperability with Python programs, enables easy coordination of image acquisition with other experimental components, and provides modular building blocks that can be used to create custom interfaces for any setup.
For more information, see description below abstracts.
ABSTRACTS AND BIOS
Igor Sokolov (Tufts) 1,2,3 *
Title:
Novel multidimensional imaging with atomic force microscopy (AFM) and machine learning image processing are key for the first use of AFM in medicine
1. Department of Mechanical Engineering, Tufts University, Medford, MA 02155, USA
2 Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
3 Department of Physics, Tufts University, Medford, MA 02155, USA
* Email: Igor.Sokolov@Tufts.edu
Abstract
The recent development of novel modes of operation of atomic force microscopy (AFM), FT-NanoDMA and Ringing Mode allowed imaging of the distribution of physical and mechanical properties of organic materials, in particular biomaterial, down to the nanoscale. In this talk, I will present a description of these two novel modes developed in my lab and give examples of the use of these modes to image/map cells and polymers. These modes were develop to address the major bottleneck of the AFM technique, repeatability robustness of the imaging. I’ll particularly focus on an application of Ringing mode modality to detect cell phenotype, to identify the presence of active bladder cancer by means of the analysis of the obtained images using machine learning methods.
Details of the presented techniques: FT-NanoDMA is a fast Fourier-transfer nano-dynamical mechanical analysis/ spectroscopy. This nanoindentation mode allows for measuring the storage and loss moduli of materials in the range up to 500Hz (the range used to describe polymers). Compared to the existing state-of-the-art nanoindentation, FT-NanoDMA demonstrates ~ 100x improvements in both spatial (down to 10nm) and temporal resolution (down to 0.7 sec/pixel). Ringing Mode is in advanced sub-resonant tapping. Compared to the existing sub-resonant tapping (such as Digital Pulse, PeakForce Tapping, HybriD, etc.), this mode allows obtaining up to 8 additional channels of information (such as adhesion height, adhesion neck height, length of molecules coating the surface, etc.), which are inaccessible by any other exiting techniques.
Bio: Dr. Sokolov’s AFM adventure started in 1987, when he encountered the first AFM made in the Soviet Union. Being trained as a quantum field theory physicist, his early AFM works (his Ph.D. thesis) were about the search of unknown fundamental forces in nature. Using AFM force measurements, he obtained much stronger restrictions on new elementary particles than was previously found from the observation of red giant stars. Later, after suggesting ideas of lifting and tapping mode, he was awarded by E.L. Ginzton International Fellowship Award from Stanford University. His interests gradually migrated to biophysics and possible medical applications of AFM. He is now a professor at Tufts University, with 190+ referred papers, including publications in elite journals like Nature, Nature nanotechnology, PRL, Advanced Materials, Materials Today, etc. He has 21 patents issued and pending, including 6 in the area of AFM related to medical applications of AFM, machine learning, new Ringing and FT-NanoDMA modes. His current research interests include physics of aging and cancer, and the AFM-related interests are AFM for Heath, with the overarching goal to introduce AFM to the medical area.
Sara Hashmi (Northeastern University)
Title:
Using optical microscopy to measure droplet and colloidal particle mechanics in confined flows
Abstract:
Bio:
Sara Hashmi is an Assistant Professor in the Department of Chemical Engineering at Northeastern University. Dr. Hashmi founded and directed the Facility for Light Scattering at Yale, a University core facility, before joining Northeastern in 2019. At Northeastern, Dr. Hashmi’s research focuses on studies of complex fluid dynamics in confined geometries, from microfluidic suspension flows to macroscopic granular flows. Investigations in the Complex Fluids Lab are largely experimental, driving flow through custom-designed devices coupled with video microscopy and a suite of image analysis tools and complementary measurement techniques. While the investigation revolves around fundamental questions, all of the research in the Hashmi Lab is geared toward better understanding of real-world phenomena, from biological and environmental flows to industrial processes.
Xingbo Yang (Department of Molecular and Cellular Biology and John A. Paulson School of Engineering and Applied Sciences, Harvard University)
Title:
A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging
Abstract:
Cells convert energy via metabolic activities to power cellular processes, to grow and divide. Defects in cell metabolism are known to associate with many diseases, including cancer, neuropathology and infertility, but the mechanisms remain unclear partly due to a lack of techniques to measure metabolic activities with sufficient spatiotemporal resolution in vivo. Fluorescence lifetime imaging microscopy (FLIM) has been applied extensively to study the metabolic state of cells and tissues with optical resolution by measuring the fluorescence intensity and lifetimes of endogenous electron carriers NAD(P)H. While these studies have demonstrated high sensitivity of FLIM of NAD(P)H to metabolic perturbations and changes in cell physiology, it remains a challenge to relate the FLIM measurements to activities of specific metabolic pathways. In this talk, I will present a technique to infer metabolic fluxes from FLIM measurements of NADH. This technique is based on the use of a coarse-grained NADH redox model that relates FLIM measurements to metabolic fluxes. Using this technique, we have discovered subcellular spatial gradients of metabolic fluxes in cells.
Bio:
I did my PhD in theoretical soft condensed matter physics at Syracuse University. Working with Cristina Marchetti, I focused my research on the mathematical and computational modeling of collective behaviors of active systems, with realizations from intracellular actomyosin cytoskeleton to epithelial tissues to animal flocks. After graduation, I did my first postdoc at Northwestern University, collaborating with developmental biologist to model cell mechanics in embryo morphogenesis. Currently at Harvard University, I am doing my second postdoc at Dan Needleman’s lab working on biophysics of cell metabolism. I am combining quantitative experimentation with theoretical modeling to develop new techniques to measure metabolic activities with unprecedented resolution and using these techniques to dissect the mechanism of flux partitioning in cells and to measure energetic costs of key cellular processes in development.
Philip Seifert (Schepens Eye Research Institute-Massachusetts Eye and Ear)
Senior Research Technologist & EM Specialist
Abstract: There are published and marketed lanthanide-based non-radioactive uranyl acetate substitutes that provide TEM contrast with low cost and minimal hazards. En bloc and post-grid staining with lanthanides (gadolinium triacetate and neodymium triacetate) was evaluated and compared to uranyl acetate for contrasting mouse ocular cellular membranes, nuclei, organelles, extracellular matrices and adeno-associated viruses in TEM.
Robert Brandon (Bruker)
Abstract:Bench-top micro-XRF systems have been used in criminal forensic labs for many years because they provide elemental analysis data similar to SEM-EDS, with the added benefits of allowing larger samples, requiring minimal sample preparation and no need for electrical conductivity, providing better limits of detection for titanium and heavier elements, and being non-destructive. This talk will briefly compare SEM-EDS with micro-XRF and provide examples of micro-XRF results.
Demonstration:
Napari-Micromanager Ian Hunt-Issak (Harvard University)
Napari-micromanager is a rapidly developing project providing Python-based, free and open-source software for operating light microscopes. It uses the core functionality from the Micromanager project but replaces the Java based user interface with one embedded in Napari - a high performance image viewer. This design allows for seamless interoperability with Python programs, enables easy coordination of image acquisition with other experimental components, and provides modular building blocks that can be used to create custom interfaces for any setup. I will demonstrate how to:
- Use Napari-Micromanger for fluorescence microscopy,
- Incorporate control of other experimental components,
- Dynamically modify data acquisition from Python,
- And use individual controls from Napari-Micromanager to create a custom GUI.
