Core Facility Day

Registration for elmi2024 includes admission to the Core Facility Day.

Taking place on Tuesday 4 June, the Core Facility Day is an integral part of the elmi experience! 

Provisional Programme

08:00 - 09:00


09:00 - 09:15


Leica Microsystems - Website 2.jpg

The Core Facility Day is kindly sponsored by Leica Microsystems

09:15 - 10:45

Session One - Tools and Resources

Session Organisers: Helena Coker (University of Oxford, UK), Gabriel Krens (IST, Austria), Roland Nitschke (Univeristy of Freiburg, Germany) & Stefan Terjung (EMBL Heidelberg, Germany)

Microscopy tools and resources are often developed at a local level and can be difficult for others to find, leading to lost time and duplication of effort. This session will focus on disseminating knowledge about existing microscopy tools and teaching resources and where to find them.

The session will include an interactive questionnaire to learn how different facilities manage their need for custom adaptations/tools, followed by presentations of selected facility tools including hardware, software and quality control solutions, and of selected teaching tools, including available teaching kits. Finally, the session will include crib talks from facilities focusing on the process of producing tools and an open forum discussion.

09:15 – 09:37 

Introduction to community tools and resources Stefan Terjung, Gabriel Krens, Helena Coker

09:37 – 09:44 

How to Create Your Own Microscopy Gizmos Robert Hauschild (IST, Austria) 

3D printing empowers everyone to create and modify microscopes and imaging accessories. This introduces the unique opportunity to extend the open-access concept from knowledge to technology, enabling researchers worldwide to use and expand upon existing models. I offer a short introduction to the hardware and software required to start creating your own sample holders, inserts, manipulators, etc. Additionally, I will present examples and explore the possibilities and limitations of 3D printing.

09:44 – 09:51 

The Image Processing Portal (IPP) Nicholas Condon (The University of Queensland, Australia)

IPP is a user-friendly, web-based GUI that connects users to institutional-based HPC for easy and efficient processing of large microscopy datasets. We have built out several workflows such as file conversion, batch scripting execution and deconvolution. With the IPP we see up to 15x reduction in processing times and far fewer user-initiated steps, speeding up workflows and research.

09:51 – 09:58 

A cloud-based database to monitor microscope performance Laurent Gelman (FMI, Switzerland)  

Performance measurements in microscopy can be properly interpreted sometimes only if compared to many measurements made on the same system over longer periods of time. The problem is: how to log easily and possibly error-free the values from metrology tests performed by multiple users, and visualize instantly all data collected in a synoptic manner? At our facility, we configured a cloud-based database from AirTable to monitor microscope performance on a weekly basis and to share this information with all our users. This intuitive and rather economical solution requires no programming skill, nor previous knowledge about databases.

09:58 – 10:03 

From community-driven idea to prototype to product/company and teaching tools Roland Nitschke, Christian Feldhaus

10:03 – 10:10 

The STEM Optics Kit Extended: education, training and prototyping Christian Feldhaus (MPI for Biology Tuebingen, Germany)

The STEM Optics kit has been developed in collaboration between German BioImaging and fischertechnik. The application for the original set is teaching optics in primary and secondary schools. However, with a few commercially available, low-cost extensions, it can be used to demonstrate and teach many advanced microscopy/ imaging principles. Configuration and modification of different beam paths on the simple optical bench system are quick and easy and can be tested in the community room. As the system is made out of simple building blocks with many degrees of freedom for assembly, it can also be used as a platform for prototyping, and we will also showcase some examples.

10:10 – 10:17 

The OpenFlexure Microscope Freya Whiteford (University of Glasgow, UK)

The OpenFlexure Microscope is a compact, fully motorised lab microscope with built-in automation. It has been replicated thousands of times, in over 50 countries and on every continent. Most of its parts can be 3D printed on basic printers, and its openly licensed design and assembly instructions have been extensively refined over seven years to ensure it is an easy and reproducible instrument to build. OpenFlexure Microscopes are found in incubators, pathology labs, field trips, community groups, and educational settings – and are increasingly used as a platform on which to implement a variety of more advanced optical microscopy techniques. We will showcase its capabilities, and highlight some activities going on in the global community that has grown up around the microscope. In the Community Room, there will be opportunities to get hands-on with some OpenFlexure Microscopes, and to see details of how they work and how they are built.

10:17 – 10:24 

Building a microscope is simple – We said Haoran Wang (Leibniz institute of Photonic Technology, Germany)

Even though yet a challenge, sharing microscopy images and their corresponding processing software is simple in comparison to recreating the hardware that acquires them. However, with the growing number of open-source electronics, low-cost optoelectronics components and a huge open-source developer and user community, building and distributing low-cost microscopes has greatly improved. In this workshop, we invite you to join a journey with the concept of open-source microscope using UC2 [1] and the Matchboxscope [2], which focus on different approaches for diverse applications. The microscopes range from several to thousand euros which can fulfill many fundamental use cases. We show you how easy it is to build a simple smartphone microscope and how the same components can be rearranged to form a complex and fully automated light-sheet microscope.

This will give a solid base to discuss the future of decentralized microscopy, and how we can form networks of data collection, storage and processing using open-source tools. Microscopy control and image processing software cannot live without their hardware counterpart and vice versa, so let’s think of them more closely together. In order to ease experience exchange, we established an online tutorial and forum to benefit the active community around the world [3].

By creating an open business model that relies entirely on open source and community building, we aim to create an example of how open innovation from science can be scaled up using open source licenses [4].
[1] Diederich B, Lachmann R, Carlstedt et al., “A versatile and customizable low-cost 3D-printed open standard for microscopic imaging”. Nature Commun” doi:10.1038/s41467-020-19447-9

10:24 – 10:30 

Joint Discussion Christian Feldhaus, Freya Whiteford, Haoran Wang

10:30 – 10:45 

Tools and resources summary and community discussion Gabriel Krens, Helena Coker

10:45 – 11:15


11:15 - 12:45

Session Two - Data Management

Session Organisers: Johanna Bischof (Euro-BioImaging, Germany), Mariana Carvalho (INL, Portugal), Susanne Kunis (University of Osnabrueck, Germany), Josh Moore (German BioImaging, Germany), Damien Schapman (PRIMACEN, France) & Caterina Strambio-De-Castillia (University of Massachusetts, USA)

As microscope capabilities have increased in recent years, so too have the volumes of data being produced, and this has resulted in a pressing need for facilities and users to have organised strategies for data management. This session will discuss different approaches for storing, analysing and sharing data as well as examples of existing data infrastructures.

The session will begin with an introduction to data management possibilities followed by talks from national and international bioimaging communities (including BioimagingUK, EuroBioimaging and BINA, amongst others) about specific data management challenges and successes. The session will end with flash talks from members of the microscopy community focusing on interesting examples of data management strategies, open-source tools for data management, and tips and tricks for effective data management.

11:15 – 11:25 Introduction to Data Management and BioImageTown Caterina Strambio-De-Castillia, Josh Moore, Matthew Hartley, Guillaume Gay
11:25 – 11:35 BioImagingUK Data Management Georgina Fletcher (BioImagingUK, UK)
11:35 – 11:45 VIB BioImaging Data Management Sebastian Munck (VIB, Belgium)
11:45 – 11:55 BINA/QUAREP Data Management Judith Lacoste (MIA Cellavie Inc, Canada)
11:55 – 12:05 France Bioimaging RTmfm Data Management Guillaume Gay (France BioImaging, France), Thomas Guilbert (INSERM, France)
12:05 – 12:15 EuroBioImaging/Global Bioimaging - Data Management Aastha Mathur (Euro-BioImaging, Germany), Bugra Oezdemir (Euro-BioImaging, Germany)
12:15 – 12:25 German BioImaging Data Management Tom Boissonnet (HHU, Germany)
12:25 – 12:35 Universiteit Leiden Data Management Katy Wolstencroft (Leiden Institute of Advanced Computer Science, The Netherlands)
12:35 – 12:36 A FAIR GUI -  a vision for easy collection and exchange of essential metadata in microscopy Roland Nitschke
12:36 – 12:37 FAIR Instruments and Facilities: persistent identification of instruments and community-defined hardware descriptions  Caterina Strambio-De-Castillia
12:37 – 12:38 The Image Data Resource: a scalable resource for FAIR biological imaging data Frances Wong (University of Dundee, UK)
12:38 – 12:39 YeastTube: Revolutionizing Microscopy Data Management with AI and Web Technologies Andrey Aristov (Institut Pasteur, France)
12:39 – 12:40 BEXIS2 – a user-friendly Platform for Microscopy Metadata Management Ivan Belyaev (Friedrich Schiller University Jena, Germany)
12:40 – 12:41 FAIR AI through FAIR data in EMBL-EBI’s BioImage Archive Matthew Hartley (EMBL-EBI, UK)
12:41 – 12:45 Data Management Summary Johanna Bischof

12:45 - 14:00


14:00 - 15:30

Session Three - Spatial Omics

Session Organisers: Oliver Biehlmaier (University of Basel, Switzerland), Marjolijn Mertz (Netherlands Cancer Institute, The Netherlands) & Jessica Valli (Heriot Watt University, UK)

Spatial omics encompasses a broad range of techniques that combine imaging of physical tissue structures with molecular characterisation within the native 3D context. This can provide new biological insight by providing data about how cells interact within their tissue environment in response to disease or therapeutics. This session will introduce the capabilities of these emerging techniques, and discuss the challenges of implementing them within facilities.

This session will include an overview of spatial omics techniques, including their capabilities and under-pinning technologies. This will be followed by talks from facilities, split into two parts. The first set of facility talks will comprise experiences of specific systems; this will aim to cover all major commercially available systems and to discuss custom-built alternatives, and will focus on challenges, tips and tricks, and will aim to inform facilities in how to choose a system.  The second set of facility talks will discuss the organisation of spatial omics facilities within microscopy facilities or as standalone entities. Finally, the session will end with a moderated discussion covering topics such as spatial omics data analysis, costs and consumables, maintenance, and user experience.

14:00 – 14:10 Introduction to Spatial Omics Oliver Biehlmaier, Marjolijn Mertz
14:10 – 14:17 Tips for using Akoya Phenocycler + Fusion and the Akoya Phenocycler + Zeiss Observer microscope Marjolijn Mertz
14:17 – 14:24 Tips for using Vizgen MERSCOPE Sheida Hadji Rasouliha (University of Basel, Switzerland)
14:24 – 14:31 Tips for using 10X Genomics Chromium X Arne Seitz (EPFL, Switzerland)
14:31 – 14:38 Tips for using Miltenyi MACSima Platform Simon Walker (Babraham Institute, UK)
14:38 – 14:45 Tips for using the GeoMX Eric Reits (Amsterdam UMC, Amsterdam)
14:45 – 15:00 Implementing Spatial Omics in Existing Facilities Arne Seitz
15:00 – 15:30 Moderated Discussion on Spatial Omics