Pre-conference workshops

AI in microscopy

Background: Recent years have given us tremendous advances in methods using artificial intelligence to solve many different tasks: The deep learning model chatGPT [OpenAI 2021] demonstrates how we can interact with computers naturally, and the Segment Anything Model (SAM) [Kirillov March 2023] has shown that most segmentation tasks can be completed given enough examples.

Content: 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. We will start with the well-known QuPath analysis program, then we will investigate Jupyter Notebooks and Python as general tools for image analysis, and finally, we will explore whether large-language models are a shortcut to image analysis in Python; and 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.

Target group: Microscope life scientists

Format: Alternating lectures and hands-on exercises. Bring your laptop. 

Participation fee includes: Lunch and refreshments.

More details:

University of Copenhagen, Amager

Contact persons: 
Prof. Jon Sporring ( 
Ass. Prof. Stine Hasselholt (

Number of participants:

Maximum 60 participants. There will be lectures and hands on exercises on people’s own laptops.


25 August, 10:00-16:00


EURO 65 incl. VAT

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.


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

Number of participants:



25 August, 10:00-17:00



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


DTU, Building 307/314, Technical University of Denmark

Number of participants:



25 August, 11:00-15:00



Organised by Bruker Nano and Fischione Instruments

Helios 5 Hydra and Spectra Ultra: a state-of-the-art duo for Materials Science

Explore Materials Science sample preparation methods using the state-of-the-art multiple ion species plasma FIB Helios 5 Hydra, imaging and spectroscopy of beam sensitive materials using the best-in-class Spectra Ultra STEM. This session comprises both talks and practices, featuring roundtable discussions of a wide range of applications of both Helios 5 Hydra and Spectra Ultra, touching base on the recent developments of cryogenic and inert gas transfer workflow of air and beam sensitive samples from FIB to TEM


What to Expect: Live Demonstrations: Witness the potential of the best-in-class Thermo Scientific Helios 5 Hydra PFIB-SEM and Spectra Ultra STEM.


Facility Tour: Explore the Core Facility of DTU Nanolab, Lyngby.


Expert Insights: Attend talks focusing on various applications of the multiple ion species plasma FIB and the ultra high resolution imaging and spectroscopy of Spectra Ultra.


Interactive Sessions: Discuss your research projects with experts and gain insights into the latest techniques and workflows using plasma FIB and Spectra Ultra.


Networking Opportunities: Connect with peers and experts during the sessions and lunch, coffee breaks


DTU Nanolab

Number of participants:



25 August, 11:30-16:00



Organised by ThermoFisher Scientific

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 Hydra Bio Plasma FIB-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, and coffee breaks.


Bella Center Copenhagen

Number of participants:



25 August, 10:30-17:30



Organised by Thermo Fisher Scientific

Leica UC ENUITY: Bringing Ultramicrotomy to the Digital Age


Explore our new microtomy platform and learn from Mr. Helmut Gnägi (Diatome), Andreas Nowak (Leica Microsystems) and Frederic Leroux (Leica Microsystems).


What to expect?

Hands-on practice, tips and tricks (trimming, sectioning, ribbon collection, array tomography, knife cleaning)

Introduction of the UC Enuity, the next generation ultramicrotome that saves you valuable time through its automated setup functions, providing state-of-the-art sectioning quality.

During this workshop we will discuss application examples that showcase how UC Enuity can be leveraged to advance ultramicrotomy processes for EM sample preparation.

A new auto approach mode that brings block face and knife together, automatically. 

Automated Trimming:

Perform ultramicrotomy tasks using UC Enuity automated functionality that eliminates the need for complex manual setup steps.

Target Trimming:

Trim your target with the help of 3D µCT data . Start 3D volume acquisition directly where it matters!

Cryo sectioning:

Learn best practices in cryosectioning and cryoplaning


CFIM, The Panum Institute

Number of participants:

Min 6 - max 10


25 August, 10:00 - 16:00



Organised by Leica Microsystems

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. 


CFIM (Core Facility for Integrated Microscopy),  Haderup Auditoriet, University of Copenhagen

Number of participants:

Max. 100


25 August,  09:00-17:00

Full-Day Workshop 

Experience Level: Beginner to Intermediate


EURO 100

Organised by the HyperSpy community