Staff Members

Steering Comitee

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

• KBC infrastructure (2022, 2023)

• Kempe foundations, GenFys Departament (Leica Stellaris 8 DIVE multiphoton; 2020)

• Nils & Dorthi Troëdssons foundation (AFM Stage; 2019)

• Kempe foundations (Atomic Force Microscope (AFM); 2019)

• UMU infrastructure grant (Cryostat, 2019)

• Kempe foundations (Leica DMi8 epifluroescence microscope; 2018)

• SLU infrastructure grant and Kempe foundations (Zeiss LSM 800 and 880 confocals; 2018/2017)

• Vinnova competence center (Vibratome, 2017)

• Kempe foundations (BD FACSAria III; 2017)

• Kempe foundations (Leica M205 FA stereofluorescence microscope; 2017)

• Knut & Alice Wallenberg foundation, project grant for “ShapeSystems” (Nikon Az-Z2 Vertical macroconfocal; 2014)

• Umu strong research environment funding (Leica HCS LSI macroconfocal; 2012)

• Knut & Alice Wallenberg foundation, equipment grant (Zeiss LSM 780 confocal; 2010)

• Vinnova competence center (general grant for the facility)

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

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..

Zeiss LSM780 CLSM with inverted stand
Zeiss LSM780 CLSM with inverted stand at UPSC.
This confocal has laser excitation lines at 405, 458/488/514, 561 and 633 nm and a 32-channel GaAsP spectral detector and two additional channels + transmission light (DIC) detector. The confocal is mounted on an inverted microscope with motorized XYZ stage and there are four objectives of 10x 0.45 dry, 25x multiimmersion, 40x/1.2 water and 63x/1.4 oil. This confocal can be used for FRAP, FRET,  colocalization studies, 3D imaging, time lapse studies with up to 8 fps at 512x512 pixel, spectral range scans, tile scans, multiposition scanning, linear unmixing, online fingerprinting, photon counting, etc.

The confocal is located in room KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4 h and each introduction is maximized to two participants. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.

Zeiss LSM 800 with airyscan
Zeiss LSM 800 with airyscan at UPSC.Arabidopsis hypocotyl stained with propidium iodine.

The confocal is mounted on an upright Axioimager.Z2 microscope with motorized XYZ stage. There are five objectives of 10x/0.45 Plan-apo dry, 20x/0.5 water-dipping N-Achroplan, 40x/1.0 water-dipping N-Achroplan, 40x/1.2 water and 63x/1.4 oil and many of them are adjusted for DIC. This confocal has laser excitation lines at 405, 488, 561 and 640 nm, 2 single GaAsP detectors, airyscan detector optimal for 40x objectives and transmission light (ESID) detector. It is also equipped with an axiocam 506 color camera and LED lamps for brightfield and fluorescence imaging.

The confocal can be used for FRAP, colocalization studies, 3D imaging, time lapse studies with up to 8 fps at 512x512 pixel, tile scans, multiposition scanning, fast panorama overview of whole sample with pyramidal imaging, setting up of complex acquisition experiments with experimental designer, imaging of both non-fluorescent dyes in combination with fluorescence etc.
The confocal is located in room KB.K2 (B2.18.51). The instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4 h and each introduction is maximized to two participants. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.

Zeiss LSM 880 with airyscan and PicoQuant Fluorescence Lifetime Imaging (FLIM), Fluorescence Correlation Spectroscopy (FCS) and FCCS
Zeiss LSM 880 with airyscan.LSM 880:
The confocArabidopsis apical hook stained with propidium iodine.al is fully motorized and built on an Axio Observer 7 inverted microscope with a scanning stage and 13 mm Z travel range. There are adjustable holders for slides, 24-98 mm Petri dishes and for standard multiwell plates. It has 6 objective lenses where most have DIC: 10x/0.45 dry Plan-Apo, 20x/0.8 dry Plan-Apo, long working distance 32x/0.85 water corr C-achroplan, 40x/1.2 water corr (good for FCS), 40x/1.2 Imm autocorr Plan-Apo for water, silicone oil or glycerine immersion, 63x/1.3 imm autocorr Plan-Neofluar for water,silicone oil or glycerine immersion.

For laser excitation there are continuous laser lines for 405, 440 (PicoQuant cw or pulsed), 458/488/514, 561 and 640 nm.
The detector unit is a QUASAR spectral detection system (2 PMT detectors and a 32-channel GaAsP spectral detector) and one airyscan detector for high sensitivity and resolution detection.

PicoQuant FLIM and FCS:
There are pulsed (also cw) lasers of 440, 485, 510 and 561 nm. Two sensitive HyD detectors for FLIM, FLIM-FRET, FCS and FCCS detection with time detection MultiHarp 150 4N. The software SymPhoTime 1+2 for analysis and data acquisition.
The Zeiss LSM 880 and PicoQuant systems are connected and synchronized.

This confocal can be used for FRAP (fluorescence recovery after photobleaching), FRET (fluorescence resonance energy transfer), colocalization studies, 3D imaging, time lapse studies with up to 8 fps at 512x512 pixel, spectral range scans, tile scans, multiposition scanning, linear unmixing, online fingerprinting, photon counting, ~2x higher resolution than standard confocal with airyscan, FLIM, FLIM-FRET, FCS, FCCS etc.

The confocal is located in room KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4-8 h and each introduction is maximized to two participants. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.

Stellaris 8 DIVEMultiphoton microscope Leica Stelaris 8 at UPSC.
The confocal and multiphoton microscope is fully motorized and built on a DMi8 inverted microscope with a scanning stage. It has a Z motion range and a Galvo stage with up to 1.5 mm moving range (Super Z range). It is a spectral system for both confocal and multiphoton imaging. There are adjustable holders for slides, 24-98 mm Petri dishes and for standard multiwell plates. As alternative to standard stage there is a cooling/heating stage from 10°C below room temperature up to 37°C for 35 mm Petri dishes. Fluorescence metal halide light source with filter cubes FITS LP, GFP BP, Y3 (red) BP. The system stands on an active antivibration table.

Objective lenses:

• HC Plan APO 10x/0.4 air, WD 2.56 mm (0.17 mm cover slip)
• HC Fluotar L 25x/0.95 W (water), LWD 2.5 mm (0.17 mm cover slip)
• HC Plan APO 40x/1.25 Glycerol with motorized correction collar - adjusted inside software, WD 0.35 mm.

Available lasers:

• 405 nm laser
• White light laser (WLL): Tunable in the range of 440-790 nm in increment of 1 nm, maximum 8 lines at a time with a minimum output power of 1.1 mW. Pulse frequency 78 MHz.
• Multiphoton laser: Tunable in the range of 690-1040 nm, 1 line at a time, 2.1 W power average, > 100 fs pulse width, adjustable diameter of laser beam, internally operated in software for easy alignment and tuning. Note that the multiphoton laser is very strong and in the invisible range, do not look directly on the laser beam (which you cannot see, but it may damage your eyes)!!!

Beam splitting system:

Acusto-optical tunable filter (AOTF) sets the correct wavelengths of the WLL and acusto-optical beam splitter (AOBS) reflects the correct laser wavelengths to the sample and transmits the rest to the detector.

Scanning mirrors:

Scanning can be done with precision using X2Y scanning mirrors or fast with resonance scanner.
The field of view can be rotated 270 degrees. Is done with an Abbe-König rotator; which allows a scan of smaller field of view compared to digital rotation that some other confocal systems have.

Detectors:
3 HyD-S detectors (can be up to 5) for confocal imaging, detection range: 410-850 nm with 1 nm precision. Highly sensitive detectors can be used in analog, reflection or photon counting (1 detected photon=1 grey level) mode.
1 HyD-S and 1PMT spectral detector for multiphoton imaging (non-descanned detectors (NDD); can add up to 4 NDD detectors), detection range: 380-800 nm.

Other features:

• Lambda scan: scan for the emission spectra with given laser line.
• LAMDA scan: scan for the excitation spectra for WLL and MP lasers.
• LAMBDA-lambda scan: scan both laser excitation and emission spectra
• Z intensity compensation during Z stack acquisition and 3D image analysis software
• Rolling average during time lapse imaging
• LAS X navigator: spiral scan overview, imaging of large samples, multiposition imaging, change of focus over image plane
• Fluorescence lifetime information can be used with TauContrast for Intensity, TauSeparation, TauGating, GateScan or TauScan to separate information based on fluorescence lifetime.
• LiveData Mode
• FRAP wizard for setting up bleaching or laser ablation experiments
• Lightning is used for high resolution imaging with direct adaptable deconvolution.

Multiphoton:
Multiphoton laser is in the infrared spectra so it cannot be seen by human eyes but is very strong and dangerous upon exposure! If the laser safety box is on you are safe, but if that is removed one must take great caution to avoid the laser beam. Use laser safety glasses or cover the laser with a laser-safe cover (not any cover, it must stop the IR laser and not catch fire).
Multiphoton needs two (2-photon) or more laser pulses to converge very close in time on the same fluorophore for excitation to occur. This only happen in a very small volume of the sample (femtoliter) in the focal plane. Hence, no need for pinhole with multiphoton as it is very unlikely to get excitation from other planes than the focus plane.
The IR light generate a lot of heat so great care must be taken with laser intensity, but bleaching is very low other than in the femtoliter area where excitation occur. The small volume and heat generation is why laser ablation, bleaching and photoswitching can be done in a specific cell or compartment (confocal shine and excite fluorophores in the whole sample causing blech in several layers).
As one does not need any pinhole it is possible to use detectors that are going directly from the objective, so called non-descanned detectors (NDD), which then conserve a lot more of the photons and thus one can get higher sensitivity (around 4x better than confocal detectors) besides that one can get light from several airy unit orders of light to somewhat increase resolution. We have one PMT and one HyD (supersensitive) detector that are NDD (two more can be added if needed and somebody wants to pay for it). Due to the sensitivity, a dark room is needed to not induce noise.

Variable beam expander:
For multiphoton laser one can adjust the laser beam to maximize laser intensity or resolution.
To maximize laser intensity one underfill objective with light leading to deeper penetration but lower resolution.
To optimize resolution one overfill objective with light (b) left).
This feature is found in Beam routing - VBE, drag the bar to the left for high power and to the right for high resolution. 

Second harmonics:
You can also look at second harmonics with MP, which is another form of light that is emitted at half the wavelength of the laser (e.g., with an 800 nm laser the second harmonics will be at 400 nm). This signal is usually weaker than fluorescence so using the HyD NDD detector is advisable. Only 20-30% of the second harmonics is going backwards the most efficient detector would be a forward detector, but we don’t have that. To know if it is second harmonics or autofluorescence etc. one can test bleaching; second harmonics does not bleach whereas fluorescence does or, move the emission detector slightly away from the half laser spot and second harmonics disappear as it has a very narrow detection window whereas fluorescence has a broader. For second harmonics one might need to increase the gain to higher than 100% (like 180%) as the MP may fry the sample if one uses too much laser.

Using it:
The Leica Stellaris 8 DIVE is located in room KB.K2 (B2.20.51). This instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4-8 h and each introduction is maximized to two participants. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.

Nikon CrEST Cicero Spinning Disks for fast imaging and an upright stand Nikon LV100ND microscope 

• Nikon NIS-Elements Advanced research (AR) software package for 6-dimensional imaging including all necessary modules for hardware control and macro programming
• Nikon LV100ND with transmitted light and intelligent 5-fold nosepiece
• Ocular tube with erected image • Motorised XY-stage and Z-focus (mounted to fine focus) 
• 4x with parfocal adapter for existing Olympus XLUMPLFLN20XW (Parfocal 75 mm / Thread M25)

Zeiss LSM 980

The Zeiss LSM 980 confocal system is mounted on an inverted AxioObserver 7 and has motorized XY stage with Z piezo for fast and accurate movement. This confocal has laser excitation lines at 405, 445, 488, 514, 561 and 639 nm. The detector system is a 32-channel GaAsP spectral detector, two additional spectral PMT channels, airyscan detector + transmission light (DIC) detector. There are four objectives of 10x 0.45 dry, 25x water with motorized correction collar, 32x/0.85 long working distance water objective with autoimmersion module, 40x/1.2 water with motorized correction collar. This confocal has AI sample finder for fast finding of sample and overview of the whole sample area that can be used for ZEN connect.
There is a black box around the stage so dark work can be performed. The system can either be operated at room temperature or with a temperature-controlled stage insert (10-40°C).

The confocal is packed with features, including regular confocal imaging with LSM plus deconvolution, Airyscan 2 with joint deconvolution for high resolution imaging (down to 90 nm lateral and 270 nm axial with a 1.4 NA objective), multiplex 4y and 8y imaging for highspeed imaging of up to 47,5 frames per second in 512x512 pixel size, (continuous laser) FCS/FCCS Fluorescence Correlation and Cross Correlation Spectroscopy and with the airyscan module dynamics profiler to study 19 FCS profiles next to each other. Dynamics profiler allows measure of flow and directionality. This confocal can be used for FRAP, FRET, colocalization studies, 3D imaging, time lapse studies, spectral range scans, tile scans, multiposition scanning, linear unmixing, online fingerprinting etc. One can do direct processing during acquisition or later.

The confocal is located in room KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes 4 h and each introduction is maximized to two participants. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.
Microscope LSM 990 ZEISS

Macroconfocals

Macroconfocals are systems built for confocal imaging of larger specimens such as insects or plant materials. They are equipped with macroobjectives which allow sharp wide-field confocal imaging.

Nikon vertical macroconfocal (AZ-C2 vertical)
Front side of vertica macroconfocal Nikon AZ-C2 at UPSC.Sample holder.Arabidopsis root cell walls stained with propidium iodine and nuclei with DAPI.


This macroconfocal is specially built for imaging of plants in gravity on 12 x 12 cm agar plates or standard slides. The system is equipped with a AZ100 horisontally mounted macroscope with option of  2x/0.2 WD 45 mm or 5x/0.5 WD 15 mm DIC  macroobjectives, a zoom range of 1-8x and diascopic or epifluorescent light (CFP, GFP, YFP and RFP) options. The samples are placed in a humidifying chamber to minimize sample drying. In addition the stage is motorized in XYZ and there is a macromanipulation holder attached to the stage. The macroscope is attached to a C2 confocal that is equipped with 405, 458/488/514, 561 nm laser lines. In addition, the system is equipped with both a filter detection system and a spectral detection system in addition to a transmission detector. This macroconfocal can be used for multicolor imaging, linear unmixing, 3D imaging, tile scans, time lapse studies, multiposition scanning, colocalization studies etc.
The confocal is located in room KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis. You are allowed to use this confocal only after passing a mandatory introduction! A basic introduction to this instrument usually takes two sessions of 2-3 h or more and each introduction is maximized to two participants. For introduction or other questions regarding this instrument, please contact Anna Gustavsson.

Analysis computers:
To alleviate the using time at the microscopes and allow data analysis with the software available at the microscopes, there are two off-site image analysis computers in the room inside the confocals. These computers are connected to the image servers so that the acquired images can be easily reached.
Computer #1: This computer has software for Zeiss ZEN black 2010, Image J, Leica LAS, photoshop and windows office.
Computer #2: This computer has software for PicoQuant SymPhoTime 1+2 for data analysis of FLIM, FLIM-FRET, FCS and FCCS. Full version of Arivis vision 3D and 4D for fast visualization and analysis of multi-dimensional images. Computers are located in room KB.K2 (B2.18.51).

Data storage on microscope server:
The data must not be stored on any of the microscopes or the analysis computers for long time as space is limited on these systems. Please move all data to the dedicated UPSC microscope server. For access to this server, contact Simon Birve. Do not contaminate the computers with viruses (high risk when using USB sticks or external hard drives).

At UPSC we have several types of sectioning equipment to make posible to use different type of samples and obtain different thicknes of sections. 

Cryostat - CryoStar NX70
Automated Cryostat for fresh and frozen material sectioning range of 1-500 μm thicknes, eqipped in CryoJane tape system. Cryostat is located in room KB.K6 (B6.24.51).

Cryostat Cryostar NX70 at UPSC.

.

Microtome: 
Fully automated scientific microtome Leica Nanocurt R for wax and resin embedded material sectioning of semi-thin sections with range betweeen 0,25-50 μm. Microtom is located in room KB.K6 (B6.24.51).

We remind you, that resins belong to allergenic compounds and one needs to have special education before strating to work with them. If you need such education please contact This email address is being protected from spambots. You need JavaScript enabled to view it.. 

Ultramicrotome
Power Tom XL for resin embedded material and ultra thin sections is located in room KB.K6 (B6.24.51).

Ultramicrotome Power Tom XL.

Microtome NanucutR at UPSC

Vibtatome:
Two machines  Leica vibratome VT1000S (Frodo and Gandalf) are used for quick sectioning and diferent histochemical staining, for  fast screening, sections range 1-999 μm thickness, they are located in room KB.K6 (B6.18.51).

Vibratome Leica VT1000S.

Glass Knives Maker EM KMR3
The Leica EM KMR3 is  easy to use glass knive maker. The balanced break method of the Leica EM KMR3 ensures perfect glass knives for ultrathin sections for EM and LM. The automatic reset of breaking wheel and the scoring mechanism to "default" after a breaking cycle avoids handling errors. Galss knives maker is located in room B6.24.51

Glass knife maker Leica EM KMR3.

 For introduction or other questions regarding those instruments, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..

UPSC has several microscopes where bright field, DIC, dark field, phase contrast and epifluorescence imaging can be performed. 

Microscopes available at UPSC:

Epifluorescence microscope Leica DMi8

The microscope is inverted, fully motorized with a scanning stageMicroscope Leica DMi8 at UPSC. and motorized focus to allow Z stack acquisition. There are seven objective lenses 5x/0.15, 10x/0.32, 20x/0.4 corr 0-2 mm DIC, 40x/0.6 corr 0-2 mm DIC, 40x/1.1 water corr DIC, 63x/1.3 glycerol corr DIC and 100x/1.32 oil DIC. The change between objectives is made with parafocality, automatic adjustment for Koehler illumination and contrasting method allowing full reproducibility between sessions. In addition, fluorescence imaging for DAPI, GFP and mCherry can be made with fast switching between brightfield/DIC and fluorescence. There are also conventional filter sets for DAPI LP and BP filter, CFP, GFP LP and BP filter, YFP, RFP, and Cy5 (only visible by camera) where the 16 individually selectable LED light sources (in the range of 365-770 nm) can be fully controlled by the software. There are holders for slides of different length, 3 cm round Petri dishes and multiwell plates. The system is equipped with a Leica DFC 7000 T color camera which is sensitive enough for fluorescence and can do imaging at 40 fps. In addition, there is an even more sensitive monochrome Leica DFC 9000GT sCMOS camera with improved signal-to-noise ratio compared to the color camera. The system can be fully controlled by the software to allow easy changes between objectives, different fluorescence/DIC/bright field settings, stage positions, focus in combination with time lapse. The system is also triggered for fast imaging possibilities.
It has LAS X navigator for easy imaging options where one can do preview overview imaging of the whole sample. This overview can then be used to select one or more interesting regions for further imaging at high resolution where tile and stitching will be automatically recognized by the software when the sample is too large to fit in one image with the selected objective. There are autofocus algorithms or manual possibility to keep focus along a sample for tile imaging, which makes it possible to “straighten out” an unevenly mounted sample. In addition, the software can do 2D deconvolution of fluorescence images or extended depth of focus for color images.
Applications: Virtually any microscopy work that can be done on an inverted stage, which does not need phase contrast or dark field.
This microscope is located in room KB.K6 (B6.22.49) This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.

Epifluorescence microscope Zeiss Axioplan 2

Poplar stem section stained for lignin detection (Mule staining).

Axioplan 2 microscope at UPSC.

The microscope is upright, manual, equipped with colour CCD camera and a range of objectives (4x-100x). Microscope is equiped in conventional filter sets DAPI, GFP/YFP LP, RFP LP, GFP, CFP and CFP+GFP.  MIcroscope is eqiped in Lumencor SOLA SM II Solid State White Light Engine LED lamp.

This microscope is located in room KB.K6 (B6.24.51) This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.

Epifluorescence microscope Zeiss AxioObserver A1m

Zeiss AxioObserver A1m at UPSC.

Fragment of poplar stem, cross section with visible tension wood.

The microscope is inverted, manual, it has equipped with colour CCD camera and a range of objectives (4x-100x) with 2 of then as long working distans objective perfect for observation of bigger objects like callus. There are holders for slides of different length, 3 cm round Petri dishes and multiwell plates.  Microscop is equipped with standard mercury bulb. This instrument is operated on an hourly fee basis. You are allowed to use this microscope only after passing a mandatory introduction! For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch.

Other available microscopes:
Zeiss AxioStar upright epifluorescence microscope equipped with standard mercury lamp and 10x-40x objectives is located in room KB.K6 (B6.20.51).
Zeiss Axioplan upright microscope equipped with colour CCD camera and computer is available to borrow from facility.
Axiovert 40 CFL inverted long working distance inverted epifluorescence microscope with holders for Petri dishes and multiwell plates equipped with standard mercury lamp and monochromatic CCD camera. located in room KB.K6 (B6.18.51).
Zeiss Standard 25 small upright microscope with two pair oculas for simuntaniosly observation by two persons.  located in room KB.K6 (B6.18.51). 

Whole cross section of poplar stem from microscope, stained for starch.

Stereomicroscopes available at UPSC:

Leica M205 FA stereomicroscope with Fluorescence

Fully motorized system with parafocal objectives of 0.63x Plan-Apo
Epifluorescence strereomicroscope Leica M205FA at UPSC.with a working distance of 67 mm and 2x/0.35 Plan-Apo with a working distance of 20.1 mm and a 0-5 mm correction ring for water pillar (or agar). The objectives are mounted on a revolving nosepiece and can achieve 4.7 - 320x zoom magnification range that corresponds to a work field diameter of 46.1 – 0.72 mm. 
It has episcopic light via gooseneck LED lamps and transmitted light via a light base that is equipped with motorized Rottermann contrast TM, brightfield and two-sided darkfield. Fluorescence by LED light source and bandpass filter sets for DAPI, CFP, GFP, YFP and RFP, in addition to long pass filter set for GFP. A DMC6200 digital pixel shift color camera is used for image acquisition. In addition, it is also equipped with a sensitive monochrome Leica DFC 9000GT sCMOS camera for improved fluorescence imaging. The stereomicroscope has ergonomic setup of ocular, tube and light base.
With this system one can do imaging of brightfield and/or fluorescence multichannel acquisition, time lapse images, 3D/Z stacks, overview images of large field of views, tile scan acquisition and stitching, spiral scan acquisition, 2D deconvolution and it has several analysis tools. 
Applications: fast screening of fluorescence zygosity on plates with fast overview imaging or ocularly, GUS overview images and then more detailed imaging over large areas using tiles and stitching etc.
The stereomicroscope is located in the room inside KB.K6 (B6.22.49). This instrument is operated on an hourly fee basis. You are allowed to use this stereomicroscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. Due to heavy usage, expect to wait 3 weeks or more for an introduction. For introduction or other questions regarding this instrument, please contact Marta Derba-Maceluch or Judith Felten.

THUNDER Model Organism

This system is built on the Leica M205FCA stereomicroscope. This is the semi-motorized version with two objectives: 1x PlanApo, with a 61.5 mm working distance, equipped with the FluoCOMBI and 5x macro, with a 19 mm working distance, giving a shift in the light axis, making the M205FCA a macroscope (Parallax free imaging), also equipped with the FluoCOMBI. The maximum magnification of this microscope is 640x, with max NA of 0.5.
The system is equipped with a TL3000ergo transmitted light base, mounted with a high precision scanning stage that can be manually operated or motor controlled without losing linearity. The Rotterman contrast and darkfield are set manually and only from one side. However, the on/off switch and the intensity are both modulated through the software and the mirror tilt (Rotterman and darkfield) is coded in the software. It is thus possible to restore settings. The system is equipped with a sensitive monochrome Leica DFC 9000GT sCMOS camera, and fast CMOS Leica K5C color camera, the light source SOLA SM (with DAPI wavelength 365 nm) and the bandpass filter sets for DAPI, GFP, CFP, YFP and RFP (some additional filters are accessible on the LeicaM205FA).
Due to the macro configuration, the FluoCOMBI needs a separate dichroic in the light path that is matched to the standard filter used. We have two of such dichroics: 1) a quad dichroic which works for DAPI, GFP, RFP and Cy5; and 2) a multiband dichroic for CFP/YFP and mCherry.
Possible applications: high magnification, high resolution imaging. The system allows high-quality 3D images of thick samples, imaging of brightfield and/or fluorescence multichannel acquisition, time lapse images, 3D/Z stacks, overview images of large field of views, tile scan acquisition and stitching, spiral scan acquisition, 2D deconvolution and it has several analysis tools. , at the same time, benefits from the speed and sensitivity of a widefield system by using an optodigital method called Computational Clearing.

Example of Computational Clearing used on THUNDER microscope, left side fluorescent picture, right side after Computational Clearing.

The stereomicroscope is located in the room inside KB.K2 (B2.18.51). This instrument is operated on an hourly fee basis (please check price tab). You are allowed to use this stereomicroscope only after passing a mandatory introduction! A basic introduction to this instrument usually takes 2 h. 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.

Microscope THUNDER model organism at UPSC

Greenhouse equipment:.

Leica MZFL III epifluorescence stereomicroscope

This microscope allows fast screening of fluorescence (filter sets for CFP, GFP, YFP and RFP). Allows 8-100x magnification. This microscope is in the greenhouse dark room on floor 2.

Stereo fluorescence Microscope Leica AFL III at UPSCArabidopsis vascula boundle staind whit Toluidine blue

Crossing stereomicroscope, Leica S9i

This stereomicroscope is suitable for 3D viewing with 12 mm depth of field and 37.7 mm object field. Zoom 6.3x-60x. Working distance 81 mm. This microscope possesses an inbuilt camera that is connected directly to a screen. An SD chip can be used to save images. This microscope is in the greenhouse on floor 2 at the photo station.

Microscope Leica S9i at UPSC

Screening stereomicroscope Leica M125C

Zoom 10.8:1 with 1x plan apo objective (8x-100x); zoom information is coupled to the software to include scale as a parameter in the image. Working distance 61.5 mm. Equipped with stage TL3000Ergo with easy maneuver of transmitted light. LED light ring with 16 switchable lamps for adjustable light from the top. Long stand. Camera 12 MP, 60 fps, computer with Las X software. This microscope is in the greenhouse on floor 2 at the photo station.

Stereomicroscope Leica M125C at UPSC

Screening stereomicroscope Leica MZ9.5

This microscope is suitable for fast screening and basic imaging, equipped with CCD camera MC190HD and LAS EZ software. The system is in the greenhouse on floor 4.

Stereomicroscope Leica MZ9s at UPSC

Basic stereomircroscope Leica M16

This stereomicroscope is suitable for screening in wilde field. The system is located in the greenhouse on floor 4.

Stereomicroscope Leica MZ16 at UPSC

Crossing stereomicroscope, Zeiss Stemi 2000-C

This basic stereomicroscope is suitable for crosses. The system is in the greenhouse on floor 4. 

Stereomicroscope Zeiss Stemi 2000 C at UPSC

More information: https://www.umu.se/en/research/infrastructure/umea-core-facility-for-electron-microscopy-ucem/

Contacts
https://www.umu.se/en/research/infrastructure/umea-core-facility-for-electron-microscopy-ucem/contacts-and-location/