Workshop 3

Modern microscopy techniques acquire an ever-increasing amount of multidimensional image data.
3D microscopy techniques, such as selective plane illumination microscopy (SPIM), easily generate multiple terabytes of raw image data in a single experiment that require tailored solutions for interactive or automated analysis.

The ACQUIFER HIVE is the established solution for efficient and safe management and storage of large image data without USB drives or network copy. The HIVE allows fast access to acquired data for swift processing and flexible analysis workflows. It is designed as a modular platform that is configured for your specific applications and will grow with your needs.

In this workshop, we will introduce the concepts of HIVE workflows, and we will present new solutions to expand existing HIVE installations to serve a higher user base and larger projects. Multi-GPU and Multi-HIVE solutions are outlined. Besides scaling in processing, concepts about data safety with large storage pools are discussed.

As part of the workshop, we offer RDP access on the centralized multi user system HIVE for testing. We encourage participants to bring their own laptops.

Please refer to our website at www.acquifer.de or call us at +49 (6221) 435 2000 for more detailed information on ACQUIFER products.

One of the core facilities’ duties is to provide end-users, usually researchers in life sciences, a fleet of microscopes at a level of performance compatible with their experiments. This is not an easy task because the performance of such devices tends to fluctuate or deteriorate over time for many reasons: misusing, aging, environment fluctuations, etc. This is especially true for high end imaging systems such as confocal or super resolution microscopes. Having access to a unique, reliable, and easy-to-use device to ensure microscopes’ performance would certainly make easier this tedious task.

To get quantitative and reproducible data, assessing the performances of fluorescence microscopes is a prerequisite before any imaging campaign. For example, system co-registration accuracy should be evaluated before any co-localization study; System field uniformity and intensity response before any study where intensity in the image matters; Spatial resolution before any study aiming at counting objects close to each other, etc.

Three years after our last presence at ELMI, we are happy to come back and present during this workshop the novelties we have developed in the meantime: improved hardware products, new analyses from 3D patterns, new analyses related to non-Argolight products, improvements in user interface and user experience, etc. Above all, the presentation aims to show how the quality control of fluorescence microscopes can be standardized with Argolight software solutions, and how the generated quality control data can be managed and centralized for later reporting.

In this workshop we will demonstrate Bruker super-resolution and light-sheet microscopy solutions (Luxendo SPIM family).
The SPIM demonstration will cover different sample types and potential applications ranging from life imaging of delicate live specimen such as organoids and embryos (mouse, zebrafish etc. ) to whole in-toto imaging of large cleared samples such es entire adult mice. We will be showing our 3D Super-resolution system, the VXL with patented 3D technology suitable for STORM and PALM, along with an integrated microfluidics system for highly multiplexed, DNA-PAINT research.

Workshop 1/4 : TruLive3D SPIM – light-sheet microscopy for live samples
Workshop 2/5 : VXL – 3D super-resolution microscopy
Workshop 3/6 : LCS SPIM – light-sheet microscopy for cleared samples

Image:
Top, left image: live zebrafish embryo H2A::GFP recorded on Luxendo MuVi SPIM LS.
Top, right image: Mitochondria stained for TOM20 with Alexa 647 and imaged with STORM.
Bottom, left image: cleared adult mouse with GFP labeled nerves and recorded on Luxendo LCS SPIM.
Bottom, right: Cleared YFP expressing transgenic mouse brain recorded on Luxendo MuVi SPIM CS

Incremental improvements in confocal imaging have assisted the flexibility of the laser scanning microscope, but these are often limited to a single acquisition mode.

Two new capabilities for the ZEISS confocal microscopes provide improvements in image quality for every imaging modality. LSM Plus works with all detectors to both improve signal to noise ratio and increase image resolution down to 120nm and Airyscan Joint Deconvolution (jDCV) uses the Airyscan technology to generate image resolutions down to 90nm. Both capabilities provide these significant image improvements without the need for additional detectors or imaging approaches. These developments boost the performance to such an extent that your confocal now provides an easy path to super resolution without needing to move to alternative imaging platforms.

This workshop will introduce the new functionalities and explore the details of how these capabilities can be easily used to gain additional insights from a wide range of specimens.

The DeepSIM is the first super-resolution (SR) microscope module that is compatible with any existing upright or inverted microscope with a camera port and is as easy to use as a confocal microscope enabling scientists to access SR data about their biological samples. Why DeepSIM? Resolution is doubled in all dimensions compared to a confocal microscope, reaching 100nm in XY and ~ 300nm in Z. In this workshop, we demonstrate that two-fold enhanced spatial resolution can be obtained with high and low magnification objective from 100X to 20X, making CrestOptics DeepSIM SR module a reliable, simple to use and affordable solution to study sub-cellular details and expand the range of applications.

#super-resolution #SIM

Fluorescent imaging can be a double-edged sword; beneficial in biological models, characterising subcellular detail and monitoring co-cultures [1], but at the same time playing havoc with the health of your cells. Livecyte’s correlative fluorescence capability enables fluorescence signal to be captured infrequently, but the signal from individual cells to be linked over time using the tracking data from frequent quantitative phase imaging; long-term fluorescence intensity whilst substantially reducing phototoxicity effects.
This workshop will guide users through Livecyte’s Analyse Fluorescence Dashboard and explore some of the unique metrics it can achieve. In particular, how we can investigate phagocytic activity in macrophages using fluorescent bioparticles in response to a cytotoxic drug cytochalasin D. The Fluorescence Dashboard in Livecyte’s Analyse software reveals single-cell metrics marking a dose dependant reduction in median fluorescent intensity of macrophages and therefore a reduction in phagocytosis.
Fluorescence is also useful in understanding subsets of cells within the same population. In this workshop we will investigate differences between differentiated and progenitor cells both in isolation and co-culture. Using the Explore page in Livecyte’s Analyse software, subpopulations of cells can be defined with gates or filters based on cell behaviour, morphology or fluorescence expression. Differentiated cells were found to be larger and have reduced motility compared to progenitor cells. It was also possible to determine changes in behaviour when cells were in co-culture compared to cells in a homogeneous population with differentiated cells proliferating at a slower rate when they are in isolation.

Presenter: Mikko Nokkonen / Evident Europe

In modern research centers more and more slides need to be scanned, with an increasing variety of formats, sample preparation and obervation techniques. Only in this way the necessary data can be obtained to understand each detail together with its context. In this workshop you will learn how the VS200 Slideview scanner provides a powerful combination of flexibility and quality to adapt to any application and “see more” of your samples. Built for speed and reliability the VS200 Slide scanner becomes the central destination for all scanning needs, taking off the burden from other non-dedicated instruments.

High-resolution microscopy of cells requires imaging chambers that are specifically tailored to your application.

Are you interested in learning about…
… easy to handle all-in-one solutions for live cell imaging?
… the advantages of using channel slides for immunofluorescence stainings?
… solutions for 3D cell culture and spheroid imaging?

Join our workshop and find the answers to these questions!

First, we will introduce a variety of ibidi chambers with different geometries and surfaces and help you to choose the products that are best suited for your assay. This will be followed by a hands-on-training where you get the chance to test a selection of our labware for 2D and 3D cell culture and imaging.

Experience Mica in action and learn how its sample-centric operation allows straightforward access to imaging for all users .
See how MICA dramatically reduces the time-to-image and training time for non-imaging specialists.
Learn how our new FluoSync technology detects four fluorophores simultaneously, in both widefield and confocal!
Discover how the whole workflow from setting up an imaging experiment to the AI powered extraction of data has been radically simplified.
See all this working directly on samples and specimens you see every day – from multi-well plate assays to large tissue sections to model organisms – all on Mica!

Cutrale, F., Trivedi, V., Trinh, L. et al. Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nat Methods 14, 149–152 (2017). https://doi.org/10.1038/nmeth.4134
·Hsiao Chiang, Daniel Koo, Masahiro Kitano et al. HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal to noise fluorescence, 12 January 2022, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-1073331/v1]

White paper: https://webcdn.leica-microsystems.com/fileadmin/global/products/Supercharge-the-way-you-work/White_paper_FluoSync_MC-0003306.pdf

Visualizing the three-dimensional architecture of complex organisms while analyzing biological processes in a whole-organ fashion are becoming the new standard in research. To provide a complete, smooth, and hassle-free 3D imaging workflow, Miltenyi Biotec covers this entire process offering solutions for sample staining, clearing and imaging. In this workshop, we will guide you through the most important steps of sample preparation, including a live demonstration, and will demonstrate how easily high quality 3D images of large samples can be acquired with our cutting-edge light sheet system, the UltraMicroscope BlazeTM.

Nikon Team introduces you to X-light V3 Spinning Disk System from Crest Optics, designed around our inverted Ti2 microscope and equipped with Lumencor Celesta 7-laser light engine, Photometrics Kinetix and Prime 95B cameras and silicone objectives.
Advanced optical design and engineering solutions developed by both Nikon and Crest Optics meet very high-end specifications required by most confocal facilities and users.
– Acquire more data in less time with a complete optical path dedicated to large field of view 25 mm
– Highly homogeneous illumination, thanks to Crest exclusive design of excitation microlenses. This allows for quantitative data acquisition and optimizes large image tilling
– Record fastest dynamics at very high frame rates, technically up to 6000 fps
– Dual camera port as standard and choose flexibility in e.g. resolution or increase imaging speed
– Push to the edge acquisition throughput with Nikon’s perfect control over 3rd party devices
– Multichannel (#7) imaging as standard with laser unit providing from 405 nm to 750 nm
– Superior optics with silicon & water immersion, high quality objectives to image in live-sample at depth and get accurate 3D data
– Nikon Software platform (NIS-Elements) covering simple to complex imaging workflows. It establishes the concept of intelligent microscope as operation and analysis, such as deconvolution, can run automatically to provide a significant gain in throughput and reproducibility. Visit NIS.ai workshop to discover how to train yourself AI for image processing tailored to your samples and applications.
Visit Crest Optics Booth and Workshops to discover their new Super Resolution add-on DeepSIM.

Bring your own sample to the conference to image it with Prospective Instruments MPX series Two-Photon Microscope. Contact us if you would like to take this opportunity.
Of course, we will also bring a selection of samples to image.

FLUCS photomanipulation is a non-invasive, all-optical method based on thermoviscous flow that allows the microscopist to induce precise microscopic flow fields inside living cells or microfluidic chambers.

During the workshop,
we present RAPP’s FLUCS add-on optical module that is compatible with all standard inverted microscopes,
we explain the working principle of FLUCS technology,
we discuss a variety of recent applications of this novel technology in the life sciences,
and we provide guidance, to optimally exploit the technology for your experiment.

www.rapp-opto.com/products/photomanipulation-systems/flucs-micro-flow-photomanipulation/

In September 2021 the United States’ Food and Drug Administration (US-FDA) has approved the first AI-based decision support system for prostate cancer diagnostics. This hallmark indicates a historic decision as it is the first time in the history of medicine that a regulatory body has accepted a software-only solution, which analyses microscopic images by using artificial intelligence!
This indicates both, that technologies reach a performance and maturity level that makes diagnostic routine applications not only possible but also feasible and that the market demand for such solutions has reached a level where it has become viable for industry to invest in the development of commercial solutions as a return on investment can be expected.
The TissueFAXS Cytometry platform incorporates Machine & Deep Learning algorithms. It can do end-point assays as well as live-cell imaging and time-kinetic experiments. TissueFAXS Cytometry also promotes tissue cytometry to a new level of quality, where complex cellular interactions can be addressed on the single-cell level but still in histological context.
In this workshop we will give practical examples of high-end tissue cytometry applications using Deep & Machine Learning in TissueGnostics’ flagship application StrataQuest.

Studying spatial protein organization or protein copy number, clustering and mobility at the molecular level is extremely important from both a diagnostic and treatment perspective. Looking at cellular structures beyond the diffraction limit with a resolution of 15-20 nm with robust quantification has been enabled with Single-molecule localization microscopy (SMLM) like STORM or PALM. ONI has created the world’s first desktop super-resolution microscope, the Nanoimager, which is designed to operate on a standard lab bench and has a footprint smaller than a piece of A4 paper, with the most intuitive and simple software interface, making it also accessible to researchers not specialized in high end microscopy techniques with one major goal: make it accessible and simple to use.

It is really important to enable users to extract quantitative information from their localization-based images. We have done this by designing a cloud-based analysis software called CODI (COllaborative DIscovery). CODI helps users analyze their single-molecule data by extracting quantitative information on protein clustering, cluster size and area, cluster density, and so much more. It enables all researchers to upload their data, share or collaborate with other scientists, whilst gaining meaningful insights about their data.

During this workshop we will perform a two-color STORM on mitochondrial samples (TOM20 and HSP60) and reveal the sub-mitochondrial compartmental organization with 20 nm resolution. The aim is to introduce SMLM imaging as a powerful tool for rapid and multiplexed characterization of cellular structures along with a visual and quantification analysis platform CODI developed by us. We will follow up the workshop with an open discussion on the wide-ranging applicability of the Nanoimager in different biological applications encompassing the field of immunology, neurobiology, cell biology and cancer.

VISIVIEW 6.0
VISIVIEW IMAGING SOFTWARE WITH NEW REALTIME 5D IMAGE ACQUISITION AND DISPLAY
VIRTEX REALTIME EXPERIMENT CONTROL

This workshop will give the listener an overview of new developments in RingTIRF technology, new features in VisiView Imaging Software and highly accurate experiment control by ViRTEx.

2. ORBITAL Ring-TIRF Technology
The VisiTIRF-ORBITAL is a compact and powerful high speed 2D galvo driven spinning Ring-TIRF laser illumination system. It offers a large and evenly illuminated field of view to enable applications such as single molecule tracking or SMLM – Single Molecule Localisation Microscopy for superresolution imaging. Full 360 degree positioning by free circular diameter or elliptical trajectory at the back focal plane of the high aperture TIRF objective offers illumination with minimal fringes or shading gradients