Pre-conference workshops

Venue:
University of Copenhagen


Number of participants:

Maximum 100 participants. There will be lectures and hands on exercises on people’s own laptops.


Time:

25 August, 10:00-16:00


Price:

EURO 100

AI in microscopy


Recent years have given us tremendous advances in methods using artificial intelligence to solve many different tasks: chatGPT [OpenAI 2021] is a deep learning model that was released in November 2022 and demonstrated how we are able to interact with computers in a natural way. The Segment Anything Model (SAM) [Kirillov 2023] is also a deep learning model which was released in March 2023 and demonstrated that given enough examples, then segmentation is a task solved.


In this workshop, the participants will 1) get a quick overview of image processing methods and their names to provide a vocabulary for large language models. 2) get hands-on experience with free or cheap tools for image analysis. Starting with the well-known Fiji analysis program, we will use large-language models to perform image analysis, and finally, we will investigate Jupyter Notebooks and Python as a general tool for image analysis.  Finally, 3) we will discuss the advantages and caveats of the three approaches and discuss what can be done easily and when to contact a data scientist.

Optical Tissue Clearing Techniques for Three-dimensional (3D) Lightsheet Imaging 


Exploring the three-dimensional organization of intact tissues (biopsies or organs) has high impact in the biomedical research field. A plethora of new tissue clearing techniques for deep imaging has emerged during the past 10 years. While the conventional preparation techniques for fluorescence confocal microscopy enable life scientists to image to a depth of 50-100 µm before light scattering degrades image quality, clearing techniques may enable imaging from millimeters to centimeters of tissue, revealing the full 3D structure of the specimen.


By changing the optical properties of the tissue to improve the light transmission in the samples, one could explore the whole organs or organisms without sectioning. In this workshop, we will focus on two major classes: water-based (RI ~ 1.33-1.4) or solvent-based (RI ~1.45-1.56) clearing methods.


The advantages and the main challenges in the state of the art clearing techniques as tissue morphology preservation, compatibility with immunelabelling and the ability to preserve fluorescent protein emission levels will be addressed.


We will demonstrate the methodology with readymade cleared samples, and the benefits of the lightsheet microscopy using the 3i Cleared Tissue LightSheet and the Zeiss LS7 microscopes. In addition, we will show briefly different approaches for the data handling and rendering using Zeiss ZEN, Huygens and Imaris.

Venue:

CFIM (Core Facility for Integrated Microscopy), Panum Institute, Building 21, floor 01, University of Copenhagen


Number of participants:

20


Time:

25 August, 10:00-17:00


Price:

EURO 25


Organised by Jana

Microstructural characterization of crystalline materials with nanometer resolution in the SEM


Learn about the latest advancements in on-axis transmission Kikuchi diffraction (TKD) and sample preparation techniques for large-area analysis. In this workshop, you will learn how to prepare electron-transparent samples that have ideal characteristics for optimal TKD analysis – large area and uniform thickness. The technique employs argon ion milling, which produces samples that are free of structural damage and amorphization. We will also demonstrate the cutting-edge On-Axis TKD technique in a field emission SEM to achieve the best spatial resolution in the analysis of nanomaterials.

 

We will review:

  • The advantages of on-axis TKD technique for crystallographic orientation mapping of nanomaterials in the SEM
  • How TKD provides quantitative and qualitative data on the crystallographic orientation down to 2 nm spatial resolution
  • How this technique can reveal the structural and functional properties of materials

Venue:

DTU, Building 307/314, Technical University of Denmark


Number of participants:

8


Time:

25 August, 10:00-15:00


Price:

EURO 25


Organised by Bruker Nano and Fischione Instruments

Exploring the nano-scale processes of life by imaging beyond the diffraction limit


Although fluorescence microscopy has had a major impact on biomedical research, the resolution barrier inherent in light microscopy restricts the ability to resolve objects smaller than 220 nm, hampering the visualization of many biological structures such as organelles. Recent innovations have circumvented the diffraction limit by applying different physical principles of light, leading to the development of four main commercially available options for extended or super-resolution light microscopy: Airy disk scanning (Airyscan), structured illumination microscopy (SIM), single molecule localization microscopy (SMLM) and stimulated emission depletion microscopy (STED) (Figure 1).


This has pushed light microscopy into resolutions that could only be achieved by Electron Microscopy before. Since their recent introduction as mainstream techniques applied to biological research, there has been a surge in the number of applications, leading to several high profile findings in fields ranging from cancer research to structural biology. Therefore, we would like to introduce a selected group of researchers to some of these techniques (Airyscan, SIM and STED), presenting them with a theoretical basis and a hands-on session, so they become familiar with their principles and can subsequently apply them to their research questions.

 

Workshop Structure:
We will have a general introduction talk, followed by a keynote speaker lecture on super-resolution, followed by the creation of four groups (Airyscan, SIM, STED, Image processing and deconvolution) that will rotate across the hands-on stations. We have all the required equipment already in-house. We will have support from Zeiss for an application specialist, who will run one of the practical sessions.

Venue:

CFIM, Blegdamsvej 3B, Panum Institute, Building 21.01, 2200 Copenhagen N.


Number of participants:

16


Time:

25 August, 09:00-17:00


Price:

EURO 100

Going Big: Volume electron microscopy for the life sciences


Explore how to apply volume electron imaging of cells and tissues at our pre-congress workshop, an ideal workshop for new and experienced researchers in volume imaging and Electron Microscopy. This session is a blend of theory and practice, featuring advanced volume electron microscopy techniques and an engaging mix of live demonstrations, expert discussions and a thorough and up-to-date overview of the different varieties of EM volume imaging workflows and tools.

 

What to Expect

Live Demonstrations: Witness the potential of VolumeScope, Array Tomography, and spin milling using the Thermo Scientific Helios 5 Hydra PFIB-SEM.

 

Virtual Facility Tour:

Explore the Core Facility for Integrated Microscopy at the University of Copenhagen without leaving your seat.

 

Expert Insights:

Attend talks from leading scientists, focusing on groundbreaking 3D volume imaging applications.

 

Interactive Sessions:

Discuss your research projects with experts and gain insights into the latest techniques and workflows in EM volume imaging.

 

Networking Opportunities:

Connect with peers and experts during the sessions and lunch, coffee breaks.

Venue:

Bella Center Copenhagen


Number of participants:

49


Time:

25 August, 10:30-17:30


Price:

EURO 25


Organised by Thermo Fisher Scientific

HyperSpy For Electron Microscopy Data Analysis Workshop

 

HyperSpy is an open-source Python library designed for multi-dimensional data analysis, particularly suited for electron microscopy. Thanks to its modular nature, there is an increasing number of packages that extend its features to different domains. Through this workshop, you will learn to leverage HyperSpy's ecosystem functionality for spectral and imaging analysis, from single spectrum analysis to large multi-dimensional datasets.

This workshop is tailored to provide a comprehensive introduction to the powerful tools available in the HyperSpy software ecosystem for advanced analysis of electron microscopy data. Whether you're new to HyperSpy or looking to expand your capabilities with its associated packages, this workshop, delivered by the developers of the packages themselves, is the perfect opportunity to get started and connect with fellow microscopy data analysis enthusiasts. 


Venue:

Haderup Auditoriet,  CFIM


Number of participants:

Max. 100


Time:

25 August,  time 09:00-17:00

Full-Day Workshop 


Experience Level: Beginner to Intermediate


Price:

EURO 100


Organised by the HyperSpy community