Microscopy

The Microscopy Facility possesses the scientific know-how and technical knowledge in advanced microscopy and image analysis to support and enhance scientific research. We also provide access to a wide variety of instruments covering from basic to advanced light microscopy, available to all research community (from NOVA Medical School and external users).

The Facility staff assists researchers in the experimental planning of light microscopy experiments, provides in-depth training for the operation of the microscopes as well as troubleshooting during microscopes operation. Additionally, support is provided in the processing, rendering and analysis of acquired datasets. If needed, custom analysis routines will be provided as a service.

For the continued high-quality service, it is our mission to keep our resources updated and our staff on top of the latest microscopy developments and techniques.

Equipments and services

EQUIPMENT

Confocal Zeiss LSM 980 with Airyscan 2
Confocal Zeiss LSM 710
Confocal Andor Spinning disk
Widefield Observer Z1 for HCS
Widefield Axioimager Z2
Stereoscope Lumar V12 with fluorescence
Stereoscope Leica MZ16A with fluorescence
Stereoscope Stereo V8 with fluorescence
Multiple smaller Stereoscopes
Workstation 1 with Imaris 10.2, Huygens 24.10, ZEN 3.1 Workstation
Confocal Zeiss cell observer spinning disk
Multiple smaller Widefield Microscopes with/without Fluorescence

SERVICES

Training in all microscopes, for independent usage
Consulting and initial scientific project/experiment planning
Consulting in sample preparation
Training in image processing software usage (Fiji, IMARIS, Icy,..)
Image processing and analysis services: Workflow automation (macros, scripting);
Image processing Workflow consulting and development.
Image processing custom software development
Consultation for a publication

Other services:

High-Resolution Image Capture and Analysis for Validation of Morphological and Expression Biomarkers
We offer high-quality imaging of biological samples—including cultured cells, organoids, animal model tissues, and human samples—using various microscopy techniques (brightfield, fluorescence, confocal, etc.). The main focus is on quantitative image analysis for biomarker validation. This includes the detection and quantification of morphological changes (e.g., cell morphology, tissue structure, organelle alterations), the localization and quantification of protein or gene expression biomarkers (via immunofluorescence or in situ hybridization), and the spatial distribution analysis of cellular or molecular elements.
The innovative aspect of this service lies in the use of automated image analysis algorithms and machine learning techniques to extract quantifiable biomarkers from complex images. For instance, the experience and ability to accurately analyse human OCT images can be applied to preclinical models or extended to the evaluation of other structures. This service transforms visual data into quantitative, statistically robust biomarkers, enabling the detection of subtle effects caused by environmental factors or immune responses.
Visual and Functional Validation of Biomarkers in 3D Models (Organoids and Tumoroids)
With the growing relevance of 3D models developed by the Cell Culture Unit, the Microscopy Facility offers image acquisition services (including live-cell imaging when applicable) and quantitative analysis of these complex structures. This enables the monitoring of development, organization, and differentiation of 3D models, as well as the validation of biomarker expression and localization related to disease or exposure, providing a clear visual representation of the effects of environmental factors or therapeutic interventions.
High-resolution microscopy is essential for exploring the structural and functional complexity of 3D models. This service enables the validation of both functional and morphological biomarkers identified in these systems, correlating protein expression or pathway activity with 3D morphology. Such capability is crucial for translating in vitro discoveries to in vivo contexts and for validating biomarkers relevant to tissues and organs.
Support and Consultancy in Experimental Design and Image Analysis for Biomarker Studies
In addition to image acquisition and analysis, the Microscopy Facility offers specialized consultancy in experimental design for imaging-based biomarker studies. This includes optimization of staining protocols (immunofluorescence, fluorochromes), selection of the most appropriate microscopy techniques, and support in the interpretation and presentation of quantified imaging data.
The added value lies in the expertise that goes beyond technical execution. By offering support in both design and data interpretation, the microscopy unit not only delivers high-quality data but also helps partners maximize the potential of their samples for biomarker discovery and validation. This ensures that visual information is used effectively to address scientific questions. Such consultancy is especially valuable for consortia with a predominantly clinical background, bridging gaps between clinical insight and experimental imaging workflows.

Image gallery

How to use

Microscopy Facility usage is open to all community. Users must register on the equipment booking platform (Agendo) - https://fcm.agendoscience.com - and request equipment permissions before using the systems.

Alternatively, for external users we can be contacted via email. Proper training is always required to use the facility resources in self service mode.