Pre-Congress Workshops, Meetings and Satellite Meetings

A number of Pre-Congress Workshops and hands-on courses will take place at CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen and DTU NanoLab, Technical University of Denmark. 

There will be a registration fee and all participants will need to register in advance to attend. Please find more information about each workshop and the registration process for each below.

Clearing techniques, revealing the organ 3D Structure

Venue: CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen
Date and Time: Sunday 23 August 2020, 10.00 - 15.00
Price: €70
Registration Process: You can register for this workshop through the main emc2020 registration system

A plethora of new techniques for tissue clearing for deep imaging have emerged during the past 10 years. While 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 centimeters of tissue, revealing the full 3D structure of the specimen. The techniques in short all match the refractive index of the sample to the surrounding medium, thereby minimizing light scattering. The methods may be divided in two major classes, water-based (RI ~ 1.33-1.4) or solvent-based (RI ~1.45-1.56). Several pitfalls to take in consideration are the propensity of tissues to swell or shrink, the compatibility with immunolabelling, the ability to preserve fluorescent protein emission levels in the buffers/solvents, or the mounting strategy as a function of the resulting tissue softness.

We will be giving an introduction to some of the different methods developed, emphasizing advantages and disadvantages, and demonstrate a few methodologies with samples in the lab as well as mounting of tissue. We will scan a few stacks of cleared samples, using the LEGOlish (a low cost homebuilt LEGO light sheet motorized microscope) and the Zeiss Z1 light sheet and look briefly at data handling and rendering using Zeiss ZEN and AMIRA.


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Organic Ice Resist Lithography: a one-tool approach to nanofabrication

Venue: DTU NanoLab, Technical University of Denmark
Date and Time: Sunday 23 August, 13.00 - 16.00
Price: €50
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Sponsored by Raith GmbH

 

 

The purpose of this workshop is to introduce a novel nanofabrication technique developed at DTU Nanolab – Organic Ice Resist Lithography. OIRL is a novel approach to Electron Beam Lithography (EBL) where instead of a conventional resist we use “organic ice” –frozen organic molecules deposited from vapor directly on a substrate held at cryogenic temperature (Fig. 1a,b,e). A focused electron beam (e-beam) induces physical/chemical changes in organic ice, so the exposed areas become non-volatile at room temperature (Fig. 1c) and remain on the substrate after warming up (Fig. 1d). Thus, the organic ice acts as a negative tone resist and warming up the substrate replaces chemical development step of conventional lithography. OIRL preserves the strengths of EBL –high spatial resolution down to few nanometers and flexibility of pattern design– and at the same time offers its own unique advantages. The OIRL instrument is based on a commercial EBL system: the Raith eLine Plus, which we have upgraded with a custom-built gas injection system and a cryostage. During the workshop we will discuss the uniqueness of OIRL, the physical and chemical mechanisms behind the process and its great potential for applications. We will also demonstrate the technique in action during a practical hands-on session.

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

Venue: CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen
Date and Time: Sunday 23 August, 09.00 - 17.00
Price: €60
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Supported by ZEISS and Leica Microsystems GmbH

 



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 250 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 an explosion in the number of applications and a large number of high profile findings happened in fields ranging from cancer research to structural biology. Therefore, we would like to introduce a selected group of researchers to these techniques, so they become familiar with the principles of these techniques and can subsequently apply them to their research questions.

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Liquid Phase Electron Microscopy

Venue: DTU NanoLab, Technical University of Denmark
Date and Time: Sunday 23 August, 12.00 - 17.00
Price: €45
Registration Process: You can register for this workshop through the main emc2020 registration system




Sponsored by DENSsolutions




The workshop will provide an online introduction to liquid cell electron microscopy, followed by an introductory class to the field and finally laboratory tour and experimental demonstration session with the “Stream” system that provides a next generation of in-situ TEM liquid system with truly controlled liquid environment and sample biasing possibilities. 

During the demonstration session we are going to introduce the latest development in the Liquid Phase Electron Microscopy (LPEM) - Stream system from DENSsolutions. This system facilitates in-situ Liquid Heating and Liquid Biasing experiments in TEM. The heart of the Stream system is a so-called Nano-Cell (Fig. 1a), e.g. a dual chip produced by Micro-Electromechanical System (MEMS) technology that forms a miniature flow cell. Unlike many other in situ liquid systems on the market, the inlet and the outlet are located directly on the bottom chip. Thin spacers surrounding the inlet and the outlet of the bottom chip and the top chip confine the liquid inside the well-defined flow micro-channel. This novelty ensures that the liquid will always flow through the sample without by-passing the region of interest and there is no need of applying an overpressure to push the liquid in-between the Nano-Chips minimizing the risk of breaking the membrane and leaking inside the chamber. Furthermore, both the inlet and outlet of the Nano-Cell can be individually pressurized, allowing the user to control the absolute pressure and the flow inside the micro-channel. The pressure controls the bulging of the membranes used for observation, enabling the user to significantly reduce the liquid thickness and thus improve the imaging quality.

The focus of the demonstration session is liquid biasing experiment. We will discuss the range of applications enabled by Stream, present the liquid biasing Nano-Cells (Fig. 1b and 1c) and the system and demonstrate its unique capabilities during an in-situ TEM experiment. We will use the liquid biasing Nano-Cell.


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Ion mill sample preparation & EBSD/TKD analysis - Using Fischione Ion Mill 1061 and Bruker QUANTAX EDS and EBSD

Venue: DTU NanoLab, Technical University of Denmark
Date and Time: Sunday 23 August, 12.00 - 17.00
Price: €50
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Sponsored by Fischione Instruments and Bruker Nano Analytics

 

 

The workshop will focus on sample preparation using ion milling for excellent EBSD analysis. Both systems capabilities will be demonstrated live during the workshop by application scientists from Fischione and Bruker Nano Analytics.

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High Pressure Freezing and Cryo Ultramicrotomy

Venue: CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen
Date and Time: Sunday 23 August, 10.00 - 16.00
Price: €40
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Sponsored by Leica Microsystems and Diatome

 

 

Leica Microsystems will give a presentation on High Pressure Freezing and follow on techniques for TEM, cryo TEM and cryo SEM.  Diatome will give a presentation discussing Ultra-Microtomy in Biology, including room temperature serial sectioning for 3D reconstruction, cryo-sectioning: sucrose infiltated samples (Tokuyasu), plus cryo-sectioning frozen hydrated samples (CEMOVIS). There will also be a hands on section which will be focussed on Cryo Ultramicrotomy with Diatome. This will include the use of diamond knives and accessories.

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Cryo TEM, Single Particle Analysis

Venue: CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen
Date and Time: Sunday 23 August, 09.00 - 17.00
Price: €50
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Sponsored by ThermoFisher Scientific

 

 

The Centre for Integrated Microscopy of the Panum Institute opens their facilities to welcome stu­dents, post­doc­toral staff, sci­en­tists, and group lead­ers from acad­e­mia and indus­try to get updated on the recent developments in Electron Microscopy Methods for Biological applications such as Single Particle Analysis (Structural Biology), Cryo Electron Tomography (In Situ Structural Biology) and Large volume Cell Biology EM techniques together with experts from Thermo Fisher Scientific. The workshop is targeting a mixed audience of experienced Cryo EM users as well as novice EM users from the field of Cell Biology and Neuro Biology. Focus will be on sample preparation, Data acquisition and data visualization, both for classical resin embedded specimen as well as for Cryogenically prepared specimen.

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Hyperspy

Venue: DTU NanoLab, Technical University of Denmark
Date and Time: Sunday 23 August, 08.30 - 17.00
Price: €80
Registration Process: You can register for this workshop through the main emc2020 registration system

Provisional Programme:
(please note, this may still be subject to change)

Time
Session Title
Format
08.30 - 09.00
Introduction to Python and HyperSpy
Talk
09.00 - 10.30
HyperSpy basics
Practical
10.30 - 10.45
Tea/Coffee Break
 
10.45 - 11.30
Model Fittin
Practical
11.30 - 12.15
EELS Analysis
Practical
12.15 - 12.30
Introduction to machine learning in EM
Talk
12.30 - 13.00
Machine Learning
Practical
13.00 - 13.30
Lunch Break
 
13.30 - 14.30
EDS Analysis
Practical
14.30 - 15.15
Big data analysis
Practical
15.15 - 15.30
Tea/Coffee Break
 
15.30 - 17.00
Running in parallel:
- Atomic resolution image analysis
- Scanning electron diffraction analysis
- Pixelated STEM/4D STEM
Practical
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AI for Microscopy

Venue: University of Copenhagen, Universitetsparken 1, Denmark
Date and Time: Sunday 23 August, 9.00 - 17.30
Price: €70
Registration Process: You can register for this workshop through the main emc2020 registration system

AI achieves state-of-the-art performance on many image analysis tasks. Although successfully applying AI tools can be tricky, high-quality results can often be obtained with relatively little effort. The main challenge when applying AI is data annotation. Compared to medical imaging, where large homogeneous datasets are annotated as part of the clinical workflow, microscopy imaging is often characterized by small datasets where the annotation is difficult and prohibitively expensive.

This workshop presents illustrative examples of successfully applying AI in microscopy and provides a tutorial on using the Trainable WEKA segmentation in Fiji, as well as hands-on exercises demonstrating tools developed at the Center for Quantification of Imaging Data from MAX IV (QIM).

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Environmental transmission electron microscopy (High-pressure microscopy - X-ray and Electron)

Venue: DTU NanoLab, Technical University of Denmark
Date and Time: Sunday 23 August, 09.00 - 17.00
Price: €100
Registration Process: You can register for this workshop through the main emc2020 registration system

In situ characterization approaches are gaining traction within both materials as well as soft matter science. This is also true for electron and X-ray microscopy. Carrying out in situ experiments requires specialized equipment and often academic labs and to some extent also commercial labs develop and engineer their own solutions. As microscopy is a highly local technique, complementary studies on a larger scale are highly beneficial for making solid conclusions on the materials problem at hand. Interfacing with such complementary setups often require further engineering. In this workshop we will discuss the possibilities and challenges we as researchers face during in situ experimentation and when interfacing to other setups and techniques. The workshop will revolve around presentations and short lab demos ending in a round table discussion where we will discuss the possibilities of the different techniques and how we can move the in situ field forward.

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Early Career Workshop

Venue: CFIM (Core Facility for Integrated Microscopy), Panum Institute, University of Copenhagen
Date and Time: Saturday 22 August, 13.30 - 17.30
Price: €50
Registration Process: You can register for this workshop through the main emc2020 registration system

 

Sponsored by Sigray Inc. and TESCAN

 

 

More information on this workshop is available here.

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Leadership and Management Skills Courses ran by hfp consulting

Core Facility Leadership and Management Course by GerBI-GMB & hfp consulting
Date: 
19 - 22 August 2020

Leadership and Management Skills Course for Scientists
Date: 
29 - 30 August 2020

Registration Process: These courses are being handled externally by hfp consulting. Please click here to register for either meeting.

 

 

 

 

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