At UPSC, we have two different 3D printers that use different printing methods and material. They can be used to print lab or pedagogical equipment like a falcon holder or a plant cell model, but also to make new objects that would help for specific experiments such as a black box for 6 well plate or customized microscopy stage inserts.

Printing time is free of charge. The material cost must be supported by the user’s PI (filament spool or resin).

3D printer Prusa i3 MK3S at UPSC

FDM 3D Printing: Original Prusa i3 MK3S (“Prusette”)

Our facility is equipped with a Original Prusa i3 MK3S, a reliable and versatile desktop Fused Deposition Modeling (FDM) printer. This technology works by melting thermoplastic filaments (specifically PLA and PETG) at temperatures exceeding 200°C and depositing them layer-by-layer to create physical objects with millimeter-level resolution.

Capabilities & Specifications:

• Build Volume: 210 × 210 × 250 mm (max printing size).
• Applications: The printer can be used to create functional prototypes, custom laboratory tools, replacement parts, and pedagogical figures of biological structures. These physical models are particularly useful for visualizing complex cellular or anatomical data captured via microscopy.

Workflow: To operate the printer, 3D designs must be converted into machine-readable G-code using the PrusaSlicer software: PrusaSlicer Downloads.

Inspiration: Explore pre-made models for biology and laboratory use:

• Printables Biology Collection
• Thingiverse Laboratory Collection

Design Your Own: If you wish to create custom models, we recommend the following tools (free version available):

• Beginner Friendly: Tinkercad (Browser-based, easy to learn)
• Professional CAD: Autodesk Fusion 360 (Advanced parametric design)

For introduction (30min), please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it..
Prusette is located in room B5-16-51 

SLA 3D Printing: Phrozen Sonic Mini 8K (“Frozen”)Phrozen Sonic Mini 8K Frozen 3D printer

For applications requiring ultra-high detail, our facility features the Phrozen Sonic Mini 8K, a Stereolithography (SLA) resin printer. This machine uses a UV light to selectively cure liquid photopolymer resin, achieving precision with an XY resolution of 22µm. This makes it ideal for fine printing.

Capabilities & Specifications:

• Build Volume: 165 × 72 × 180 mm (max printing size).
• Precision: 22µm XY resolution with adjustable layer thickness ranging from 10µm to 300µm.
• Applications: The printer can be used for printing intricate or small objects, micro-fluidic devices, and fine structures that require smooth surfaces and details.

Workflow & Resources: To prepare a model for printing, the 3D design must be sliced into layers This process generates the specific file format required by the printer.

Software Download: Chitubox Official Site

Post-Processing: To ensure the quality and durability of resin prints, we provide a dedicated Anycubic Wash & Cure stationAnycubic Wash Cure station at UPSC. This unit automates the cleaning of uncured resin and the final UV curing process, ensuring parts are safe to handle and dimensionally stable.

Location: Both the "Frozen" printer and the Wash & Cure station are located in Room B6-18-51.

For introduction (1 hour), please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it..

Prior to the introduction to Frozen, one needs to have special education before starting to work with resin as it belongs to allergenic compounds. If you need such education, please contact Marta Derba-Maceluch.

Data Storage is aviable by UPSC Bioinformatics Facility. There is no posibilty to store data on microscopes computers. 

Label-free, non-invasive mechanical imaging of living plant tissues in 3D

The Brillouin microscope at UPSC enables high-resolution, three-dimensional mapping of the mechanical properties of living plant cells and tissues without physical contact, labelling, or sample preparation. By measuring the interaction between light and acoustic vibrations inside a sample (the Brillouin shift, Fig. 1 A and B), this instrument provides direct, quantitative information on viscoelastic properties such as stiffness and compressibility at cellular and subcellular resolution.

Unlike surface-bound techniques such as atomic force microscopy (AFM), Brillouin microscopy captures mechanical information throughout the sample volume. It is particularly suited for studies where mechanical properties change dynamically, such as during growth, cell differentiation, or responses to environmental stress.


Principles of Brillouin microscopyFigure 1: Principles of Brillouin microscopy. A. The interaction of light from a laser (green) and sound (phonons, black arrows) causes light scattering. B. Depending on the mechanical properties of the sample, the scattered light will have different frequency and intensity. C. The Brillouin microscopy technique uses a confocal microscopy coupled to a Brillouin spectrometer to direct the laser light beam to a specific point of the sample, obtaining a measurement of the mechanical characteristics (stiffness) of this point with nanometric resolution. A and B adapted from Antonacci et al., 2020.

Instrument Overview

The system is based on the CellSense Discoverer™ Brillouin microscope, integrated with a Zeiss LSM 780 confocal microscope (Fig. 1C). It combines a fibre-coupled 780 nm laser with low phototoxicity, a multi-stage dispersive spectrometer, and an advanced sCMOS detector to deliver high-sensitivity measurements with a free spectral range of 15 GHz. This allows detection of subtle changes in mechanical properties, with continuous calibration ensuring precision and reproducibility across experiments.

The system operates fully automatically, from alignment and calibration to data acquisition and analysis, making it suitable for users without extensive optics experience. Data can be collected from a defined point, a two-dimensional area, or an entire three-dimensional volume, and correlated with optical or fluorescence images for structural and genetic context. Brillouin microscope at UPSC Applications

Applications

Brillouin microscopy is a powerful tool for plant mechanobiology and cell wall research. Its ability to image 3D mechanical maps non-invasively (Fig. 2) makes the Brillouin microscope particularly valuable for long-term live imaging and for studying structures where physical contact methods are unsuitable. At UPSC, it is used to:

• Quantify changes in cell wall stiffness and viscosity during growth and development.
• Monitor mechanical responses to environmental stresses such as salinity, drought, or temperature fluctuations.
• Investigate how genetic modifications affect tissue mechanics in crops and trees.
• Study mechanical signalling in processes such as cell adhesion, lateral root formation, or pathogen interaction.
• Correlate mechanical properties with fluorescent markers or structural features through combined Brillouin and confocal imaging. 

While the system at UPSC is primarily used for plant science, Brillouin microscopy is increasingly applied across diverse areas of biology and materials research. Its label-free, contactless nature and high spatial resolution make it a versatile tool for:

• Cell biology: Measuring stiffness differences between cellular compartments or tracking mechanical changes during differentiation and morphogenesis.
• Organoid and tissue studies: Mapping viscoelastic properties in 3D to study tissue development, disease progression, or regeneration processes.
• Biomedical research: Characterising mechanical changes associated with fibrosis, tumour growth, or neurodegeneration in model systems.
• Materials science: Investigating mechanical properties of polymers, hydrogels, and bio-inspired materials at micrometre resolution.

These applications highlight the broader potential of Brillouin microscopy as a bridge between mechanics, biology, and materials science.

Technical Specifications

• Excitation source: 780 nm fibre-coupled laser, 200 mW output, frequency-stabilised with a Rubidium absorption cell
• Detection: Multi-stage dispersive spectrometer with cooled 4.2 MP sCMOS camera
• Measurement range: Free spectral range ≥ 15 GHz (Brillouin shift up to 7.5 GHz)
• Integration time: Millisecond range for live samples
• Compatibility: Fully integrated with Zeiss LSM 780 confocal microscope
• Software: Automated setup, calibration, and workflow-guided data acquisition and analysis

Access and Training

The Brillouin microscope is part of the UPSC microscopy facility located in room KB.K2 (B2.18.51) and available to both internal and external users. Training is provided by facility staff, and support is available for experimental design, data acquisition, and analysis.

For enquiries and bookings, please contact the UPSC microscopy platform or Laura Bacete This email address is being protected from spambots. You need JavaScript enabled to view it. 

Laser capture microdissection (LCM) is an automated sample preparation technique which uses a focused laser to cut and a pulsed, defocused laser to "catapult" a specific tissue sample from a slide into a collection tube. It allows the identification of specific substructures or cell types and their precise removal from the original tissue without causing damage. This technic allows for the non-contact isolation of single cells or specific cell groups from a heterogeneous mixture, making it possible to downstream microgenomics applications such as analyse of DNA, RNA, and proteins from a pure and uncontaminated sample. 

At UPSC Microscopy Facility we have Zeiss PALM system equipped in objectives 5x 10x 20x 40x 63x 100x and Pulsed Solid-Stat Laser 355 nm (UV-A)  less harmful for DNA, RNA and protein and Live cells. 

LCM is located at room KB.K6 (B6.22.49) on 6th floor. for introduction please contact This email address is being protected from spambots. You need JavaScript enabled to view it.. 

Staff Members

This email address is being protected from spambots. You need JavaScript enabled to view it., Research Engineer
Marta Derba-Maceluch, Staff Scientist
This email address is being protected from spambots. You need JavaScript enabled to view it., Post Dock
This email address is being protected from spambots. You need JavaScript enabled to view it., Stuff Scientist  

Steering Comitee

Stéphane Verger, Docent
This email address is being protected from spambots. You need JavaScript enabled to view it., Professor
Laura Bacete, Assistant Professor
This email address is being protected from spambots. You need JavaScript enabled to view it., Assistant Professor
Marta Derba-Maceluch, Staff Scientist
This email address is being protected from spambots. You need JavaScript enabled to view it., Research Engineer

• Vinnova competence center (general grant for the facility)
• Knut & Alice Wallenberg foundation, equipment grant (Zeiss LSM 780 confocal; 2010)
• Umu strong research environment funding (Leica HCS LSI macroconfocal; 2012)
• Knut & Alice Wallenberg foundation, project grant for ”ShapeSystems” (Nikon Az-Z2 Vertical macroconfocal; 2014)
• Kempe foundations (Leica M205 FA stereofluorescence microscope; 2017)
• Kempe foundations (BD FACS Aria III; 2017)
• Vinnova competence center (Vibratome, 2017)
• SLU infrastructure grant and Kempe foundations (Zeiss LSM 800 and 880 confocals; 2018/2017)
• Kempe foundations (Leica DMi8 epifluroescence microscope; 2018)
• UMU infrastructure grant (Cryostat, 2019)
• Kempe foundations (Atomic Force Microscope (AFM); 2019)
• Nils & Dorthi Troëdssons foundation (AFM Stage; 2019)
• Kempe foundations (Leica Stellaris 8 DIVE multiphoton; 2020)
• KBC infrastructure (2022, 2023,2024,2025)
• Kempe foundations, ERC (LSM 980; 2023)
• Novo Nordisc Foundation, Microscopy infrastructure (Nikon CrEST Cicero Spinning Disks; 2023)
• Kempe foundations, UMU (Brillouin microscope; 2024)
• Kempe foundations (BD FACS Melody; 2025)
• Kempe foundations, ERC (FLAMME LSM 990; 2025)

An Atomic Force Microscope is a device (Fig. A panel) that uses a cantilever (thin and narrow flexible plate) with a sharp or spherical tip in order to touch a sample. Touching of the sample allows the measurement of the mechanical properties of the sample. As the cantilever approaches and then indents the sample, the cantilever is first unaffected and later on bends as the force increases. This bending is precisely measured using a laser pointed to the cantilever, and measuring the deflection of this laser with a detector, as the cantilever bends (Fig. B panel) The force applied by the cantilever during the indentation, can be calculated in order to output the force-distance curves and the sample’s Young’s modulus, a measure of the stiffness, can be obtained. Another key features of the Atomic Force Microscope is the capacity to perform a very fast x-y scan of the surface of a sample to form an image from the mechanical information acquired. This image can be a 3D surface of the sample scanned by the AFM or a “stiffness” map of the sample based on the stiffness (young’s modulus) value measured at every pixel. Such image can range from the size of a whole tissue to the molecular and even close to atomic level. AFM thus allows a “mechanical” imaging of samples, providing invaluable information for our understanding of biological systems. The AFM can be used to probe the cell wall stiffness, the turgor pressure of a cells as well as for investigation of surface architecture.

Panel A - head of the AFM. Panel B - Principle of operation of the AFM.

Our AFM,  NanoWizard® 4 XP BioScience with Vortis^TM2 Advanced​ version SPM Controller, HybridStage^TM, DirectOverlay^TM 2 software module and QI^TM- Advanced 2 software module,  is equiped in high precision motorized stage and the associated software that allow both the automated screening of multiple samples placed on a same sample holder as well as the imaging of large samples by the “tilling” of adjacent scans of a same samples taken one after the other.
Picture of AFM microscope at UPSC facility

The AFM is located in room KB.K3 (B3.16.51). The instrument is operated on an hourly fee basis. You are allowed to use this AFM only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4 h and is followed by asistance of experience personel. For introduction or other questions regarding this instrument, please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it..  

AFM is equiped with macroconfocalLeica LSI HSC. Macroscope of this system is equipped with an option of 2x/0.234 WD 39 mm or 5x/0.5 WD 19 mm macro objectives and a zoom function of 0.63 – 9.2x, alternatively a 63x/1.3 oil objective can be used. The macroscope has brightfield with Rottermann tilted illumination and fluorescence filter cube sets for DAPI, CFP, GFP, and RFP. This confocal has laser excitation lines at 405, 488, 561 and 635 nm and a one channel spectral detector where up to 8 sequential scans can be made for multi-imaging applications. The software of this confocal can be used for either single image acquisition (LAS AF software) or for custom made automated high content screening (LAS AF MATRIX), where parameters as multicolor imaging, 3D imaging, tile scans, time lapse studies, multiposition scanning, sample tracking, colocalization studies can be performed and it also has autofocus function. In addition, there are holders for 12x12 cm agar plates, microscope slides, multiwell plates, or small round Petri dishes.

Fluorescence Activated Cell Sorter (FACS). 
BD FACS Aria III Flow Cytometer with Software BD FACS SDiva v 7.0
Fluorescence-activated cell sorting (FACS) instrument at UPSC, Aria III Flow Cytometer.





UPSC owns a BD FACS Aria III Flow Cytometer, BD Biosciences.  This instrument can be used to sort cells, isolated protoplasts and organelles like chloroplasts and mitochondria, based on autofluorescence or labelling by fluorescent marker molecules.
The system consists of three major components: a fluidics cart (supplies sheath and cleaning fluids and collects waste from the cytometer), a benchtop flow cytometer and a workstation. Most of the cytometer functions are operated from within BD FACSDiva software version 7.0.  Our system includes four lasers: a 405 nm (violet), a 488 nm (blue), a 561-nm (yellow-green) and a 633 (red) in an X-mount optical plate configuration, two octagon and two trigon detector arrays. Each detector houses dichroic and bandpass filters, which steer and filter the emitted light, and photomultiplier tubes, which detect light signals. Additionally our equipment accommodates a next-generation flow cell optimized for four laser beam spots and integrated nozzles, available in four sizes (70, 85, 100 and 130 μm) for analysis of a variety of particle sizes. The devices that can be installed in the sort collection chamber facilitate samples sorting according to their volume. There are possibilities to sort into 1.5 ml eppendorfs up to 15 ml falcon tubes. Sorting in microscopy slides can be also achieved as well as single cell sorting into multi-well plate. The loading and collection chambers of our BD FACS Aria III are adjustable in terms of temperature facilitating handling of a variety of sensitive samples.

It is possible to work with this equipment only in form of colaboration. With all questions of wish to wokr with FACS, please contac Ioanna Antoniadi


FACSMelody™ Cell Sorter
Fluorescence-activated cell sorting (FACS) instrument at UPSC, Melody

The FACSMelody™ Cell Sorter is automated instrument ,setup eliminates or simplifies routine tasks. It is easy to learn and use with minimal training required for effective operation. Built upon proven BD FACS™ Technology with a consistent track record of reliability and quality BD FACSChorus™ Software guides researchers throughout the entire cell sorting process. 

• The system is typically ready in less than 17 minutes, maximizing uptime
• Fluidic startup automatically de-bubbles the stream
• Instrument settings, gates and sort settings are available and retrievable from saved experiments
• Compensation is conveniently computed automatically from the results of compensation controls
• High sensitivity and resolution to detect and sort dim cells and rare cells and resolve adjacent populations such as low-antigen density cells, small particles and DNA cell cycles

Intavis InsituPro VSi automated system
InsituPro VSi machine at UPSC.

The Intavis InsituPro VSi, located in room B6-50-51, is a system for performing automated in situ hybridization, immuno-histochemistry labelling, or dehydration/rehydration series in samples for microscopic imaging in a high throughput manner with high reproducibility and eliminated pipetting errors. This machine is a base unit complete with reagent racks, pipetting unit, sample holders and PC based operation software. The machine performs all the following steps: rehydration of fixed specimens, permeation, post-fixation, pre-hybridization, hybridization with individual probes or antibodies, blocking, antibody incubation, post-hybridization washes, as well as the dehydration/rehydration series of other procedures for sample preparation.
For introduction or other questions regarding this instrument, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..