SPAOM 2025

Abstract

Ensuring quantifiable and reproducible microscopy data is essential to monitor the performance of the microscope over time, and to guarantee the accuracy and reproducibility of results. Among the most common procedures for this assessment are the monitoring of the illumination power and quality, the detection performance and the optics performance, often obtained by measuring the Point Spread Function (PSF) which provides information of the effective lateral and axial resolution. The PSF’s size, shape, and symmetry, when compared to the theoretical ideal resolution, provide a comprehensive assessment of the optical setup, including the objective. This, in turn, impacts image quality and the accuracy of subsequent image data analysis.

In this workshop, we will show and discuss how to measure laser power and demonstrate how to prepare and acquire tetraspeck beads’s slides, how to visually inspect them and record PSF images and how to analyze the data obtained using an open-source plugin in FIJI (MetroloJ_QC). We will look at essential metrics such as: Nyquist-Shannon sampling, image quality, shape, size and symmetry of the PSF and the parameters that may influence the shape of the PSF. 

Abstract

Super-resolution microscopy techniques have reshaped our view of biological organization at the nanoscale, but they often involve sophisticated hardware and software tools. What if you could achieve super-resolution without a super-resolution microscope? Expansion Microscopy (ExM) makes this possible by physically enlarging biological samples, allowing nanoscale structures to be imaged with standard optical microscopes. The concept is elegantly simple: instead of super-resolving your target of interest, you physically expand your sample so that its structures become larger than the diffraction limit and can be imaged on a conventional microscope.
In this workshop, we will explore the principles and workflow behind ExM, discuss the latest developments and practical considerations, and demonstrate how to apply it to your own samples. Participants will gain a practical understanding of how to design and implement ExM experiments, expanding both their imaging toolkit and their biological insights.

Abstract

This workshop introduces a practical framework for assessing the impact of imaging core facilities, combining quantitative metrics with qualitative storytelling. 

Participants will explore complementary sets of indicators: Key Performance Indicators (KPIs), which track infrastructure, user engagement, and financial performance; and Socio-Economic Indicators (SEIs), which capture broader contributions such as training, collaboration, and public visibility. 

Drawing on international best practices developed by Global BioImaging, the workshop will include breakout discussions and tools for aligning measurement strategies with institutional missions and stakeholder priorities. 

Attendees will leave equipped with tools to evaluate and communicate the value of their facilities more effectively, advocate for resources, and contribute to a shared culture of recognition within the imaging community.

Abstract

High-content screening (HCS) has long been established as a robust approach for drug discovery, particularly within industry. In recent years, however, it has also become an essential tool in biomedical research, enabling automated, quantitative analysis of complex biological systems through microscopy.

This workshop will provide a practical, hands-on overview of HCS applications that extend beyond traditional drug screening, with a focus on cell phenotyping and the study of 3D cellular models such as organoids and spheroids. Participants will gain insights into how HCS can be effectively integrated into diverse experimental contexts.

The program will cover the full workflow from sample preparation, pilot assay design, and optimized cell seeding and staining protocols to image acquisition and analysis. Key topics will include image segmentation strategies, feature extraction, and an overview of widely used software tools for HCS data processing. We will also address practical aspects of data treatment and interpretation, including preprocessing and filtering, assay quality assessment, statistical analysis, dimensionality reduction, and graphical representation of results.

Designed for researchers aiming to implement HCS protocols beyond conventional applications, this session will encourage experience sharing, address common challenges, and highlight useful resources within a collaborative setting.

Abstract

Researchers interested in functional imaging face significant practical hurdles ranging from designing and adapting behavioral paradigms for restrained animals to selecting suitable microscopy and data handling strategies. In this workshop, we will address these issues and discuss techniques aimed at solving them, and will provide participants with a forum for discussing their own challenges. We will use larval zebrafish as a target model, whose optical transparency and tractability provide unprecedented access to brain-wide neural dynamics.

In the first part, we will focus on integrating behavioral stimulation and readouts during imaging, including precisely providing and synchronizing visual, acoustic, and mechanical stimuli, capturing behavioral outputs such as tail or eye movements, and strategies for adapting freely moving behaviors to head-restrained animals, including the design of closed-loop experiments. We will also approach sample preparation, design of imaging chambers, and restraining techniques for zebrafish larvae.

In the second part, we will discuss fluorescence microscopy trade-offs: we will compare 2-photon, light-sheet, and light-field microscopy, and analyze their limitations when applied to functional imaging of behaving fish. We will also discuss pipelines for data collection and strategies for handling the large data streams produced by high-speed cameras and other hardware used in these imaging setups.

Keywords: Brain-wide functional imaging, behavioral stimulation, practical trade-offs, data handling