IM-02:
Unsupervised Quantification of large EELS datasets
Teaser:
EELS advanced considerably in past decades with more and higher quality data obtained by state of the art spectrometers. Extracting EELS information relies on user interaction which is time consuming and poses reproducibility risks. In this talk I demonstrate a fully automatic workflow resulting in fast and reliable results, without the sweat.
IM-03:
Progress in atomic resolution 3D phase-contrast imaging
using 4D-STEM
Teaser:
Computational microscopy allows us to overcome limits imposed by imaging hardware. In this talk, I will present several milestones in overcoming the limits of electron microscopy of light-element contrast and depth of field at atomic resolution, allowing us to solve atomic structures in ever-increasing volumes with atomic resolution.
IM-03:
Breaking Resolution Limits with Ptychography using Topological Materials
Teaser:
Developments in direct electron detectors and algorithms for image reconstruction have formed a new generation of “computational lenses.”
Using a computational lens approach, we can extract phase information and reconstruct images that go beyond the resolution of aberration-corrected electron microscopes.
This work can be extended to uncovering new physics in topological condensed matter systems and provide accessible sub-angstrom resolution imaging capabilities for institutions that lack the funding or facility to host expensive, sensitive equipment.
IM-04:
Advancing instrumentation and workflow for efficient cryogenic and low dose phase contrast imaging, spectroscopy, and crystallography
Teaser:
Novel instrumentation combined with streamlined workflow enables new possibilities in Cryogenic phase contrast electron microscopy of quantum materials at liquid helium temperature with swift cool-down and long hold time in conjunction with in situ biasing capability Cryo-STEM-EDS determination of elemental enrichment in vitrified cellular structures within a correlative light and electron microscopy workflow. Low dose serial electron crystallography of hydrated soft matter enhanced by synchronised fast precession unit.
IM-04:
Humphry Davy wrote, in 1812: “Nothing tends so much to the advancement of knowledge as the application of a new instrument.
Teaser:
We have developed several new instruments, which are contributing to the “advancement of knowledge”. They include a secondary electron (SE) STEM detector that has produced atomic resolution images of many different types of surfaces, and a High Energy Resolution Monochromated EELS System (HERMES), which is enabling vibrational studies of hitherto unobservable phenomena in the electron microscope.
IM-05:
Simulations of phonon and magnon EELS/EEGS including dynamical effects and multiple inelastic excitations
Teaser:
Recent developments in STEM instrumentation enabled the STEM-EELS to explore new areas of physics, such as atomic vibrations at unprecedented spatial resolution.
Interpretation of these experiments calls for new theoretical and simulation methods. Resulting recent developments in simulations of STEM-EELS of phonons and magnons will be presented.
IM-05:
Electron and x-ray spectroscopy for real-space electronic structure
mapping in superconducting nickelates
Teaser:
Core-level spectroscopy is a powerful tool across myriad fields of materials research due to the access it provides to quantitative measurements of charge distribution, electronic structure, and bonding. Here I will highlight two advanced spectroscopies which add a further component of real-space mapping: STEM-EELS to localize at the atomic scale and sNIXS to directly resolve charge density distribution.
IM-06:
Exploiting dynamical diffraction theory in the crystal structure determination from 3D electron diffraction data
Teaser:
Taking the dynamical diffraction effects into account is a prerequisite for quantitatively fitting electron diffraction data. Incorporating these effects in the intensity calculation permits extracting fine details about crystal structures, including partial and mixed occupancies, charge density effects and absolute configuration of chiral species.
IM-06:
Data analysis workflows to measure material properties and structure using 4D-STEM
Teaser:
Modern detectors can record millions of diffraction patterns in each
4D-STEM experiment. I will demonstrate how our py4DSTEM code can efficiently and robustly characterize metallic alloys, complex ferroelectric oxides,
2D heterostructures, soft matter samples, and other materials.
IM-07:
Quantifying nanoscale diffusion phenomena using in situ TEM
Teaser:
Join us as we delve into the world of quantitative diffusion studies using chip-based in situ heating in TEM.
We will unravel the intricate dynamics of surface diffusion driven dewetting and follow the random walks of individual impurity atoms inside a crystal at atomic resolution.
IM-08:
From coherent amplification to quantum sensing in electron microscopy"
Teaser:
Recent breakthroughs involving quantum interactions of free electrons spawned an exciting new field: free-electron quantum optics.
We developed a platform for coherent free-electron interactions and demonstrated the first instance of coherent amplification in electron microscopy. Our experiments show a 20-fold contrast enhancement compared to conventional electron near-field imaging, resolving peak field amplitudes of few W/cm^2, in combined time-, space-, and phase-resolved measurements.
Our vision is to develop a microscope that can go beyond conventional imaging of matter to also image the quantum state of matter and probe quantum correlations between individual quantum systems.
IM-09:
Nano-chemical Imaging and Spectroscopy at the Single-molecule Level
Teaser:
The Ruggeri Lab develop and apply nanoscopic microscopy and spectroscopic technologies to study
biomolecular process in life and disease at the single molecule scale, as well as characterising advanced functional surfaces and materials.
IM-10:
Coupling Machine Learning with Electron Videography to Study Nanoscale Dynamics and Three-Dimensional Heterogeneity.
Teaser:
I will discuss our efforts in developing various machine-learning based imaging and data collection methods to facilitate the characterization of complex nanomaterials using liquid-phase TEM, electron tomography, and these two combined.
IM-11:
Prospects of nanofluidic cavities for cryo-EM sample preparation
Teaser:
Micro-electromechanical systems (MEMS)-based nanofabrication technologies hold promise to automate the cryo-EM sample preparation
workflow and to unlock the potential of cryo-EM for 4D structural biology.
IM-12:
Enabling discovery by in-cell structural biology
Teaser:
Technological breakthroughs in cryo-electron tomography unlock an enormous potential for system-spanning discovery in structural cell biology
IM-13:
Array tomography enables correlative volume electron microscopy and spatial transcriptomics”
Teaser:
Among all volume electron microscopy (EM) approaches, Array Tomography (AT) provides the unique advantage of tissue section restoration. This enables sample reinspection - an ideal feature for correlative and multimodal approaches. Here we present novel AT workflows that combine volume scanning EM with spatial transcriptomics and electron tomography and show their application in neurobiology.
IM-13:
Multiplexed 3D imaging of single-cell organization and tissue morphology in the multicellular intestinal organoid
Teaser:
Organisms develop within the physical context of their external environment. Molecular signals and physical properties or constraints provide external conditions with which the developing organism interacts and to which it responds. This dynamic reciprocal interaction results in and is required for morphogenesis and self-organization. Thus, a mechanistic understanding of emergent tissue-scale phenomena, such as tissue shape and patterning, require spatial quantification methods that can link single-cell properties and interactions to tissue-scale measurements. To address this need for a multiscale spatial analysis method, we developed scMultiplex, a bioimage analysis method that combines spinning disk confocal fluorescence microscopy, machine learning, parallelized image processing, and optimized imaging and staining protocols to quantify whole tissue shape, cell composition, and molecular expression in 3D. We use mouse small intestinal organoid development as a model multicellular system that self-organizes from a single cell into a complex 1,000+ cell structure. Specifically, the full single-cell composition of the fixed organoid is imaged and segmented in 3D, with molecular expression, cell type markers, and cell states identified with immunostaining. Cells are spatially linked across iterative rounds of staining and imaging to achieve multiplexing of ~10-20 protein markers. Organoid tissue shape features are also extracted from a reconstructed surface mesh using a machine learning approach. We thus apply scMultiplex to thousands of organoids to link cell type composition and spatial arrangement to tissue shape emergence and uncover mechanisms of intestinal morphogenesis. This approach can be applied to diverse multicellular systems to address fundamental questions in developmental and systems biology on emergence of higher-level organization from single-cell behavior.
IM-14:
Near isotropic, high-resolution multi-beam scanning transmission electron microscopy with iterative milling
Teaser:
Multi-beam scanning transmission electron microscopy (mSTEM) of broad ion beam (BIB)
milled 250 nm thick sections is a fast and reliable vEM method suitable for the acquisition of mm³-sized samples.
It produces near isotropic, high-resolution stacks of each section by deconvolution of series of iteratively BIB-milled mSTEM images.
IM-16:
Precise targeting for volume electron microscopy, a multimodal approach.
Teaser:
This talk will describe the targeting methods that are developed at EMBL. They rely on 3D maps built from fluorescence microscopy or X-ray imaging, and on specific workflows to accurately and semi-automatically approach the regions of interest prior to EM imaging. Example applications will show how to image selected regions of interest in multiple specimens including model and non-model organisms.
