Community Room Schedule

Joint Workshop presenting three Microscopy Optical Tool Kits

14:30 – 15:30 BST, 5 June 2024 ‐ 1 hour

elmi Community Room Workshop

The STEM Optics Kit Extended: education, training and prototyping
Christian Feldhaus, Max Planck Institute for Biology, Tübingen, Germany

The STEM Optics kit has been developed in a 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 is 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.

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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.

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Building a microscope is simple – We said
Haoran Wang, Leibniz Institute of Photonic Technologies (IPHT)/openUC2 GmbH, Jena, 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 an open-source microscope using UC2 [1] and the Matchboxscope [2], which focuses on different approaches for diverse applications. The microscopes are ranged 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].

Keywords: Modular Microscopy, UC2, ImSwitch, Matchboxscope, 3D printing, Remote Controlled Microscopy

[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
[2] https://matchboxscope.github.io/
[3] https://openuc2.discourse.group/
[4] https://openuc2.com

Global BioImaging: Accelerating Collaboration and Innovation through Data Dialogue

15:40 – 16:40 BST, 5 June 2024 ‐ 1 hour

elmi Community Room Workshop

Aastha Matur, Euro-BioImaging, Heidelberg, Germany

This one-hour workshop will give the participants a chance to learn about and contribute to the current global landscape of image data sharing, showcased by Global BioImaging and Horizon Europe project, foundingGIDE. By fostering sharing and coordination among global networks, we aim to democratise access to quality image data. Through discussions on data exchange and sharing, we'll identify strategies to align diverse approaches, fostering seamless collaboration and aiming to drive transformative innovation. Let's cultivate a shared understanding of best practices, bridging isolated initiatives to create an ecosystem where collective progress thrives.

QUAREP-LiMi Working Group 5 - PSF measurement and analysis

17:10 – 18:10 BST, 5 June 2024 ‐ 1 hour

elmi Community Room Workshop

Orestis Faklaris, Biocampus, CNRS, France & WG5 Group Members

Measure the Point Spread Function (PSF) of a microscope. The PSF is one of the key quality control elements of a microscope. Frequent measurements, done with the same tools, methods, protocols, and calculating robust metrics, can ensure the reproducibility of the scientific measurements done for biological experiments. During this workshop, we are going to show the participants how to mount a bead slide, how to perform an acquisition, and then how to analyze the PSF with open-source tools. We will give some troubleshooting for PSFs that have a strange shape or are far from the theoretically expected size. At this workshop, we are going to show the protocols and metrics that are defined in the framework of the QUAREP-LiMi consortium's WG5.

Hands-on REMBI annotations using OMERO

14:30 – 15:30 BST, 6 June 2024 ‐ 1 hour

elmi Community Room Workshop

Tom Boissonnet, Heinrich Heine University Düsseldorf, Germany

The Recommended Metadata for Biological Images (REMBI) serve as a valuable guide for researchers in determining how to annotate their microscopy data effectively. In this workshop, we will demonstrate their utilization during a microscopy project using the data management system OMERO. We will explore the optimization of data organization using datasets and tags, facilitating an efficient annotation workflow. Furthermore, we will look at a batch annotation workflow, essential for High-Content-Screening experiments, consisting of importing metadata from generic CSV files. Finally, we will illustrate how our REMBI annotations can be re-used during figure creation with OMERO.figure.

RMS Application Coaching & Personal Mentoring Schemes

15:40 – 16:40 BST, 6 June 2024 ‐ 1 hour

elmi Community Room Workshop

Joelle Goulding, University of Nottingham & Georgina Fletcher, BioImaging UK and Royal Microscopical Society

The Royal Microscopical Society offers 2 different mentoring schemes, application coaching and personal mentoring. Application coaching focuses on creating expert pairings to develop hard-skills and personal mentoring is aimed at developing soft-skills. These schemes are for microscopists and are led by microscopists and supported by the PDTFIG (professional development and training focussed interest group (RMS)). Mentees are welcomed from any employment sector and job level. We recruit our mentors from the wide, international microscopy community.  Please come along and find out about the schemes, find out about mentoring and what it’s like to be a mentee or a mentor. There will be a short presentation to introduce the schemes, which will be repeated halfway through the session. There will also be the opportunity to talk to mentees and mentors who have taken part in the scheme so please drop by and have a chat!

www.rms.org.uk/opportunities/professional-development/mentoring-schemes

QUAREP-LiMi Working Group 2 - Detection system performance - Camera topics

17:10 – 18:10 BST, 6 June 2024 ‐ 1 hour

elmi Community Room Workshop

Britta Schroth-Diez, Dresden, Germany & WG2 Group Members

The QUAREP-LiMi Working Group 2 “detection system performance” presents its achievements and ongoing work. The current achievements include the finalization of the agreement between different stakeholders (major scientific camera and/or microscope manufacturers, academia users) on a general metadata model on area detectors. Furthermore, the current status of protocols for measuring basic camera parameters such as conversion factors (system gain), read noise, dynamic range, and dark signal non-uniformity (DSNU) will be presented, along with some practical on-site measurements on microscopes and subsequent analysis. The focus will be on the ongoing work to automate the workflow from measurement via analysis to the presentation of the results.