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UMCG Microscopy and Imaging Center (UMIC)

 Microscopy infrastructure to support state-of-the-art research. Facility
Microscopy infrastructure to support state-of-the-art research.
UMIC offers training and access to advanced microscopy and image processing to researchers worldwide.

UMIC is part of microscopy.nl, including the NWO-roadmaps (NEMI/EMPower and NL-BioImaging) and the Network for Pancreatic Organ Donors with Diabetes (nPOD).

The innovationniche of UMIC is developed in the Giepmans lab: large-scale EM (Nanotomy), ColorEM and Raman imaging techniques implemented in biomedical research.

Discover our research

Get started at UMIC

Training for each instrument and registration as UMIC user is mandatory.

    • Register by creating an account for BookedScheduler
    • EM is always preceded by an intake to evaluate feasibility & approach
    • Training is provided by UMIC staff only
    • Training is obligatory for each microscope
    • Training  appointment via email: [email protected]
    • Get access to the facilities and the  reservation system following successful training and registration
    • Do not use of equipment without prior training or booking

  • Reservations

    • Can be up to two weeks ahead,
    • During office hours max. 3 hours/day
    • Outside office hours for longer periods only by experienced users (ask UMIC staf).
    • Note the IncuCyte frequency booking restrictions : Image per :  half hour or multiples thereof.
    • Ask us for specials (courses/ demo’s etc) and exception that may be needed!

    Cancellations

    • Cancel your reservation in the booking system
    • If possible, notify the next user
    • The hourly fee will be charged for no-shows
    • If you are ≥ 15 minutes late, we may  re-assign the instrument 

  • Learn more about UMIC - rules and fees.

  • UMIC offers two courses: Cellular Imaging Light and Cellular Imaging Advanced for PhD students, Postdocs, Technicians and Internship students.

    See here for more information and registration.

  • If you present data obtained at UMIC (papers or presentations), please acknowledge the UMCG Microscopy and Imaging Center as follows:

    "Part of the work has been performed at the UMCG Imaging and Microscopy Center (UMIC), which is sponsored by

    if:
    then:
    Zeiss Supra55 ATLAS/EDX
    … ZonMW grant 91111.006
    Zeiss LSM7/780 confocal
    … NWO 175-010-2009-023
    CLEM/ Cryo-EM/SECOM
    … STW Microscopy Valley 12718
    Leica HPF/ FS
    … NWO 91116005
    TissueFAXS
    … NWO 40-00506-98-9021
    CIQTEK SEM
    … HTRIC/Ubbo Emmius fund (UMCG/RUG)
    ONI Nanoimager
    … HTRIC/Ubbo Emmius fund (UMCG/RUG)
    FAST-EM OR nanotomy data
    … the Netherlands Electron Microscopy Infrastructure (NEMI NWO 184.034.014) 
    OMERO or LM data
    … NL-BioImaging Infrastructure (NL-BI; NWO 184.036.012)
    Other
    … the UMCG

     

    Sent us a copy of your publication ([email protected]).

Electron Microscopy, Nanotomy and ColorEM

  • Supra 55 Scanning Electron Microscope (Zeiss)

    • Available detectors: SE2, in-lens BSD, 5Quadrant retractable BSD, STEM, EDX
    • Special applications:
      • Large area image acquisition with ATLAS software (Nanotomy)
      • CLEM with SECOM microscope (fluorescent light microscope inside the SEM)
      • ColorEM by using EDX detection in Life Sciences
    Supra 55 Scanning Electron Microscope (Zeiss)

  • TFS TalosF200i Transmission Electron Microscope

    • The TalosF200i is a 200 kV FEG Scanning/Transmission electron microscope S/TEM
    • It is equipped with a Ceta 16M camera for TEM imaging and a HAADF detector for STEM imaging
    • Two symmetrically positioned Dual Bruker XFlash6 100mm2 EDS detectors for sensitive elemental detection
    • Software and hardware for 3D tomography acquisition of TEM images as well as for 3D EDS images
    • MAPS software for large-area mosaic acquisition

  • EDX detector X-max 150 (Oxford Instruments)

    • A 150 mm2 Silicon Drift Detector mounted on the Zeiss Supra 55 reaches sensitivity levels sufficient for use not only in material sciences but also in life sciences

  • Dual Bruker XFlash6 100mm2 EDS

    • Two symmetrically positioned Dual Bruker XFlash6 100mm2 EDS detectors for sensitive elemental detection are mounted on the TFS TalosF200i Transmission Electron Microscope”
       

  • ATLAS 5 Large Area Imaging (Zeiss/Fibics)

    • An external scan generator connected to the Zeiss Supra55 SEM can automatically record multiple tiles up to 32k x 32k pixels. These tiles can be stitched, which results in very large fields of view (i.e. millimetres) with nm resolution
    • Sample holders are available, allowing multi-sample imaging of up to 11 TEM grids or 9 SEM samples
    • Data are stored using a LAN network connected to two offline PCs on which the acquired data are being stitched and exported, either as a BigTIFF or as an HTML file. This will be put on our server

  • Delmic FAST-EM

    • Optical scanning transmission EM with 64 parallel scanning beams
    • Fast acquisition of large-scale nanotomy (2D) or serial section array tomography (3D)
    • EM sections should be collected on special scintillator substrates
       

  • SECOM (Delmic)

    • A light microscope that can be put into the Supra 55 SEM by replacing the door of the vacuum chamber
    • This allows for simultaneous detection of photons and electrons (SE2 or In-Lens BSD)
    • Applications in Correlative Light and Electron Microscopy (CLEM) and Cathodoluminescence (CL)

  • SEM4000X Scanning electron microscope (Ciqtek)

    • Field emission gun (FEG) electron source
    • Available detectors: Secondary electrons, BSD, STEM, EDX
    • Applications:
      • Large-scale mosaic acquisition (nanotomy)
      • ColorEM by using EDX detection for life sciences

EM sample preparation equipment and sectioning

  • Ultramicrotome UC7/FC7 (Leica)

    • Two room temperature ultramicrotomes are available for cutting semi-thin and ultra-thin sections
    • For training purposes, a camera together with a TV screen can be mounted
    • EM Rapid Milling Device (Leica)
    • For the fast milling of plastic embedded samples, an EM Rapid (Leica) milling device is available

  • Leica VT1000S Vibratome

    • This vibratome can cut sections of 1 µm up to 999 µm
    • Applications:
      • Brain research
      • Tissue slice cultures
      • Immunolabelling
      • EM sample preparation

  • Sputter coater ACE600 (Leica)

    • With the High Vacuum sputter coater ACE600, samples for SEM can be sputter-coated with a metal (Pd/Au or Cr) to make them conductive
    • Thickness can be monitored with a quartz thickness monitor
    • Also thickness controlled carbon coating of samples or formvar grids (to make these hydrophilic) is possible
    • And a third option is Glow Discharge, mainly used to make surfaces hydrophilic
    Leica EM ACE600 - sputter coater

  • Leica Tissue Processor

    • For fully automated and semi-automated resin embedding of EM samples

  • Leica Artos 2D ultramicrotome

    • Room temperature ultramicrotome that automatically collects serial-section ribbons for array tomography (3D) purposes

(Confocal and super resolution) microscopy for live cells/tissues

  • Zeiss LSM 7 MP

    • STAND
      • Zeiss Upright Microscope Axio Examiner
    • OBJECTIVES
      • Plan-Neofluar 5x/0.16 M27 (WD=18.5 mm)
      • W Plan-Apochromat 20x/1.0 DIC (WD=1.8 mm), UV-VIS-IR and VIS-IR
      • W Plan-Apochromat 40x/1.0 DIC (WD=2.5 mm), VIS-IR
      • C-Achroplan 32x/0.85 W Corr VIS-IR, (WD=1.1 mm at D=0.17 mm) (D=0-0.17 mm)
    • EXCITATION
      • 2 Photon: 680-1080 nm tunable
      • OPO 2 Photon: 1000-1280 nm tunable
      • Wide-field 3-channel fluorescence
    • DETECTION
      • External detection module BiG incident light (reflection), 2 channels
      • External detection module PMT DC/transmitted, 2 channels
      • Camera: AxioCam MRm Rev. (1.4 megapixels, pixel size: 6.45 μm x 6.45 μm)
    • STAGE/INCUBATION
      • Incubator XL DARK S1 (temperature control)
      • Universal mounting frame
      • Tiling, z-stack, positions, and time lapse possible in different combinations
      • Adapted to intravital imaging
    • SOFTWARE
      • ZEN black, 3D rendering included

  • Zeiss Cell Discoverer 7

    • STAND
      • Zeiss Cell Discoverer high-content microscope with LSM900 confocal head
    • OBJECTIVES
      • Plan-Apochromat 5x/0.12 (WD=5.1 mm)
      • Plan-Apochromat 20x/0.35-0.8 (WD=2.2 mm) Autocorrection*
      • Plan-Apochromat 50x/1.2 water (WD=0.84 mm) Autocorrection* and automatic water immersion
      • These objectives are used in combination with a 0.5x, 1x and 2x Optovar lens
      • Possible magnifications: 2.5x, 5x, 10x, 20x, 25x, 40x, 50x, 100x
      • * 20x and 50x objectives are automatically corrected for coverslip/plate bottom material and thickness
    • EXCITATION
      • Confocal: 405, 488, 561, 640 nm diode laser lines
      • Widefield excitation:
        • Colibri 1: 385, 470, 567, 625 nm
        • Colibri 2: 420, 520, 590
    • DETECTION
      • Confocal:
        • 1 Airyscan 2 detector with fast, high S/N, and high/super-high resolution
        • 2 PMT detectors
      • Widefield:
        • Axiocam 506 B/W camera, 2752 × 2208 pixels
    • STAGE / INCUBATION
      • Fully-automated XYZ stage
      • Almost all multiwell plates will fit
      • Insert for 3.5/6 cm petri dishes
      • Insert for 2 incubation boxes
      • Insert for 2 microscopy slides
      • Temperature control
      • CO2 and O2 level control
      • Software and hardware autofocus (definite focus)
      • Tiling, z-stack, positions, and time lapse possible in different combinations
    • SOFTWARE
      • ZEN blue acquisition, image analysis
      • Cell Profiler analysis
    • This system has a coupling with a ThermoFisher Cytomat incubator for 42 plates via a PAA robot

    • STAND
      • Leica DMi8 CS Inverted microscope with fully motorized objective nosepiece and fluorescence filter cube change
    • OBJECTIVES
      • HC PL APO 10x/0.40 CS2
      • HC PL IRAPO 20/0.75 W
      • HC PL IRAPO 40x/1.10 W CORR
      • HC PL APO 63x/1.40 OIL CS2
    • EXCITATION
      • 405nm UV laser 50mW
      • White Light Laser adjustable 440-790 nm, pulsed
      • CRS Laser picoEmerald S incl. EOM
      • Light source EL 6000
    • DETECTION
      • Spectral Confocal Module based on prism with high sensitivity multiband detection system
      • AOBS beamsplitters
      • 2x Power HyD S
      • 2x Power HyD X
      • SRS Detector TLD
      • CARS detection
    • EXTRA FEATURES
      • Stellaris Falcon (Fluorescence Lifetime Imaging)
      • Stimulated Raman Scattering (SRS)
      • Coherent anti-Stokes Raman Scattering (CARS)
      • Two-photon imaging
      • Second Harmonics
    • STAGE / INCUBATION
      • Automated x,y,z stage.
      • SuperZ Galvo Stage
      • Okolab incubator Temp and CO2 controlled
        • Autofocus Focus with AFC
    • SOFTWARE
      • LAS X acquisition
      • FALCON flim imaging
    Leica Stellaris CRS

  • DeltaVision Elite

    • STAND
      • Inverted Olympus IX71 Stand
    • OBJECTIVES
      • PLAPON 60x oil, 1.42, WD 0.15 mm (Olympus)
      • UPLFLN 40x oil, 1.3, WD 0.2 mm (Olympus)
      • UPLSAPO 100x oil, 1.4, WD 0.12mm (Olympus)
      • PLANAPO 40x dry 0.95
      • UPlanSAPO 20x dry 0.75 WD 0.60 mm (Olympus)
    • EXCITATION
      • 7 colours DV light SSI (Lumencor ultrafast solid-state illumination, allowing 1ms exposure time), 280 to 680 nm
      • LED transmitted light module
      • 4-laser Photokinetics module, 405, 488, 568 and 640 nm for FRAP
    • DETECTION
      • Pco.edge sCMOS camera; pixel size 6.5 μm x 6.5 μm, 2560x2160 pixels
      • Speed: 400 fps at 512x512, 200 fps at 1025x1025
    • STAGE/INCUBATION
      • Environmental chamber, temperature, and CO2 control
      • Ultimate focus module
      • Automated flexure stage
      • Live cell speed option: allows multicolour imaging without filter change
    • SOFTWARE
      • SoftWoRx 6 acquisition and integrated deconvolution software (on a Linux CentOS 6.3 platform)
      • Workstation with one 30'' monitor

    • STAND
      • Leica DMI 8 Inverted microscope with fully motorized objective nosepiece, stage and fluorescence filters change
    • OBJECTIVES
      • N PLAN 5x/0.12 PH0 dry
      • N PLAN 10x/0.25 PH1 dry
      • HC PL APO 40x/0.95 CORR dry
      • HC PL APO 40x/1.30 OIL CS2
      • HC PL APO 63x/1.40-0.60 OIL
      • HCX PL APO 100x/1.40-0.70 OIL
    • EXCITATION
      • LED 8 light source
      • Excitation: 395, 438, 475, 511, 555, 575, 635, 730nm
    • EMISSION
      • Filter cube CYR71010/11525416
      • Excitation: 436/28, 506/21, 578/24, 730/40
      • Dichroic: 459, 523, 598, 763
      • Emission: 473/22, 539/24, 641/78, 810/80
      • Filter cube DFT51010/11525418, size P
      • Excitation: 391/32, 479/33, 554/24, 638/31
      • Dichroic: 415, 500, 572, 660
      • Emission: 435/30, 519/25, 594/32, 695/58
      • Extra emission filters: 460/80 535/70 590/50 642/80 100%
    • DETECTION
      • K8 Camera;  95% quantum efficiency (QE) back-thinned CMOS sensor
    • STAGE / INCUBATION
      • Automated high precision (Quantum) x,y,z stage with autofocus
      • OKOlab Cage incubator , Temperature and CO2 controlled
    • SOFTWARE
      • LAS X /Thunder acquisition, includes:
        Instant Computational Clearing (ICC) for removal of out of focus background
        Small Volume Computational Clearing (SVCC) ICC for z-stacks
        Large Volume Computational Clearing (LVCC) 3D ICC and deconvolution
    Leica thunder

  • ONI nanoimager super resolution microscopy

    • Applications:
      • PALM, dSTORM, PAINT
      • Extracellular vesicles imaging
    • Exitation: 405, 488, 561, 640 nm laser lines
    • Detection: Emission channels 498-620, 662-710 nm
    • Dichroic split: 640 nm
    • Incubation
      • Temperature control
      • CO2 control
    ONI nanoimager

Light sheet microscopy for live cells/tissues/organisms

    • STAND
      • Leica DMI 8CS DLS inverted microscope with fully-motorized objective nosepiece, fluorescence filter cube change, and Digital Light Sheet option
    • OBJECTIVES
      • Detection objectives: 25x, 10x
      • Illumination objectives: 5x, 2.5x
    • EXCITATION
      • 405nm UV laser 50mW
      • White Light Laser, adjustable 470-670 nm, pulsed
    • DETECTION
      • DFC9000 GTC DLS sCMOS camera (up to 70 fps, 2048 x 2048)
    • STAGE/INCUBATION
      • Automated XYZ stage. No incubation available yet
    • SOFTWARE
      • LAS X acquisition
    Leica SP8X

    • STAND
      • Lightsheet 7 KMAT microscope
    • OBJECTIVES
      • W Plan-Apochromat 10x/0.5 detection
      • W Plan-APO 20x/1,0 DIC detection
      • lumination Optics Lightsheet 7 5x/0.1 (left and right)
      • Illumination Optics Lightsheet 7 10x/0.2 (left and right)
    • EXCITATION
      • 405, 445, 488, 561, 638 nm diode laser lines
    • DETECTION
      • 2 pco.edge 4.2 sCMOS Cameras
    • STAGE / INCUBATION
      • Fully automated xyz stage
      • Temperature controlled
      • CO2 levels controlled
      • Holders for capillaries
      • Holder for fixed specimen
      • Tiling, z-stack, positions, time lapse in different combinations possible
    • SOFTWARE
      • ZEN Black acquisition,
      • ZEN Blue 3D reconstruction & image analysis
    Zeiss LS7

High-content (confocal) fluorescence microscopy for live cells

  • Zeiss Cell Discoverer 7

    • STAND
      • Zeiss Cell Discoverer high-content microscope with LSM900 confocal head
    • OBJECTIVES
      • Plan-Apochromat 5x/0.12 (WD=5.1 mm)
      • Plan-Apochromat 20x/0.35-0.8 (WD=2.2 mm) Autocorrection*
      • Plan-Apochromat 50x/1.2 water (WD=0.84 mm) Autocorrection* and automatic water immersion
      • These objectives are used in combination with a 0.5x, 1x and 2x Optovar lens
      • Possible magnifications: 2.5x, 5x, 10x, 20x, 25x, 40x, 50x, 100x
      • * 20x and 50x objectives are automatically corrected for coverslip/plate bottom material and thickness
    • EXCITATION
      • Confocal: 405, 488, 561, 640 nm diode laser lines
      • Widefield excitation:
        • Colibri 1: 385, 470, 567, 625 nm
        • Colibri 2: 420, 520, 590
    • DETECTION
      • Confocal:
        • 1 Airyscan 2 detector with fast, high S/N and high/super-high resolution
        • 2 PMT detectors
      • Widefield:
        • Axiocam 506 B/W camera 2752 × 2208 pixels
    • STAGE/INCUBATION
      • Fully automated XYZ stage
      • Almost all multiwell plates will fit
      • Insert for 3.5/6 cm petri dishes
      • Insert for 2 incubation boxes
      • Insert for 2 microscopy slides
      • Temperature control
      • CO2 and O2 level control
      • Software and hardware autofocus (definite focus)
      • Tiling, z-stack, positions, and time lapse possible in different combinations
    • SOFTWARE
      • ZEN blue acquisition, image analysis
      • CellProfiler analysis
    • This system has a coupling with a ThermoFisher Cytomat incubator for 42 plates via a PAA robot

  • IncuCyte S3 Live-Cell Analysis System

    • For easy imaging and analysing of live cells over days to months inside an incubator
    • OBJECTIVES
      • 20x
        • Image resolution: 0.62 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 0.88x0.65 mm
      • 10x
        • Image resolution: 1.24 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 1.75x1.29 mm
      • 4x
        • Image resolution: 2.82 microns/pixel
        • Image size: 1536x1152 pixels
        • Field of view: 4.34x3.25 mm
    • FLUORESCENCE FILTERS
      • Green:
        • Emission wavelength: 524 nm; passband: [504,544] nm
        • Excitation wavelength: 460 nm; passband: [440,480] nm
      • Red:
        • Emission wavelength: 635 nm; passband: [625,705] nm
        • Excitation wavelength: 585 nm; passband: [565,605] nm
    • BRIGHTFIELD
      • HD Phase Imaging in grey values
    • DETECTION
      • Camera type: Basler Ace 1920-155um
      • Sensor type: CMOS
    • STAGE/INCUBATION
      • Temperature- and CO2-controlled environment; the whole instrument is installed inside a Panasonic MCO-230AIC incubator
      • The stage can hold six multiwell plates at the same time. The stage is fixed; a microscope unit is travelling underneath it to scan the wells, or parts thereof. 2D only
    • SOFTWARE
      • The IncuCyte can be controlled from any network location with unlimited, free licences to be obtained from the UMIC
      • Basic analysis software is included

  • IncuCyte S3 Live-Cell Analysis System

    • For easy imaging and analysing of live cells over days to months inside an incubator
    • OBJECTIVES
      • 20x
        • Image resolution: 0.62 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 0.88x0.65 mm
      • 10x
        • Image resolution: 1.24 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 1.75x1.29 mm
      • 4x
        • Image resolution: 2.82 microns/pixel
        • Image size: 1536x1152 pixels
        • Field of view: 4.34x3.25 mm
    • FLUORESCENCE FILTERS
      • Green:
        • Emission wavelength: 524 nm; passband: [504,544] nm
        • Excitation wavelength: 460 nm; passband: [440,480] nm
      • Red:
        • Emission wavelength: 635 nm; passband: [625,705] nm
        • Excitation wavelength: 585 nm; passband: [565,605] nm
    • BRIGHTFIELD
      • HD Phase Imaging in grey values
    • DETECTION
      • Camera type: Basler Ace 1920-155um
      • Sensor type: CMOS
    • STAGE/INCUBATION
      • Temperature- and CO2-controlled environment; the whole instrument is installed inside a Panasonic MCO-230AIC incubator
      • The stage can hold six multiwell plates at the same time. The stage is fixed; a microscope unit is travelling underneath it to scan the wells, or parts thereof. 2D only
    • SOFTWARE
      • The IncuCyte can be controlled from any network location with unlimited, free licences to be obtained from the UMIC
      • Basic analysis software is included

  • IncuCyte S3 Live-Cell Analysis System

    • For easy imaging and analysing of live cells over days to months inside an incubator
    • OBJECTIVES
      • 20x
        • Image resolution: 0.62 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 0.88x0.65 mm
      • 10x
        • Image resolution: 1.24 microns/pixel
        • Image size: 1408x1040 pixels
        • Field of view: 1.75x1.29 mm
      • 4x
        • Image resolution: 2.82 microns/pixel
        • Image size: 1536x1152 pixels
        • Field of view: 4.34x3.25 mm
    • FLUORESCENCE FILTERS
      • Green:
        • Emission wavelength: 524 nm; passband: [504,544] nm
        • Excitation wavelength: 460 nm; passband: [440,480] nm
      • Red:
        • Emission wavelength: 635 nm; passband: [625,705] nm
        • Excitation wavelength: 585 nm; passband: [565,605] nm
    • BRIGHTFIELD
      • HD Phase Imaging in grey values
    • DETECTION
      • Camera type: Basler Ace 1920-155um
      • Sensor type: CMOS
    • STAGE/INCUBATION
      • Temperature- and CO2-controlled environment; the whole instrument is installed inside a Panasonic MCO-230AIC incubator
      • The stage can hold six multiwell plates at the same time. The stage is fixed; a microscope unit is travelling underneath it to scan the wells, or parts thereof. 2D only
    • SOFTWARE
      • The IncuCyte can be controlled from any network location with unlimited, free licences to be obtained from the UMIC
      • Basic analysis software is included

(Confocal/fluorescence/super resolution) microscopy for fixed cells and tissues

  • Leica SP8 confocal microscope

    • STAND
      • Leica DMI 6000 inverted microscope with fully-motorized stage, objective nosepiece and fluorescence filter cube change
    • OBJECTIVES
      • HC PL APO CS 10x/0.30 dry
      • HC PL APO CS2 40x/1.3 oil
      • HC PL APO CS2 63x/1.4 oil
    • EXCITATION
      • 405nm UV laser 50mW
      • 488nm blue laser 20mW
      • 552nm green laser 20mW
      • 638nm red laser 30mW
    • DETECTION
      • Spectral Confocal Module based on prism with high-sensitivity multiband detection system
      • LIAChroic beam splitters
      • Two confocal detection channels for reflection and fluorescence with tunable bandwidth and central wavelength in continuous and independent form for each channel
      • One detection channel for transmitted light (DIC)
      • Maximum scanning resolution of 8192x8192 pixels with a dynamic range of 12 bits per channel
      • Maximum scanning speed of 7 frames per second, 512x512
      • Maximum scan field: 21.2 mm diagonal
    • STAGE/INCUBATION
      • Automated XYZ stage, no incubation
    • SOFTWARE
      • LAS X acquisition

  • Leica 4000B fluorescence microscope

    • STAND
      • Leica 4000B upright microscope with digital camera and motorized fluorescence filter cube change
    • OBJECTIVES
      • 63x/1.4-0.6 HC PL APO oil
      • 40x/1.0-0.5 PL FLUOTAR oil
      • 20x/0.5 HC PL FLUOTAR
      • 10x/0.3 HC PL FLUOTAR
      • 5x/0.15 HC PL FLUOTAR
      • 2.5x/0.07 N PLAN
    • EXCITATION
      • EL6000 light source
      • Filters:
        • LPA (DAPI)
        • L5 (GFP-FITC)
        • TXR (Texas Red)
        • Y3 (Cy3)
        • Y5 (Cy5)
    • DETECTION
      • Leica DFC3000 G camera
    • STAGE/INCUBATION
      • Manual XYZ stage, no incubation
    • SOFTWARE
      • Leica LAS 4.3 acquisition

    • STAND
      • Leica DMI 8CS inverted microscope with fully-motorized objective nosepiece, and fluorescence filter cube change.
    • OBJECTIVES
      • HC PL APO CS2 40x/1.3 oil
      • HC PL APO CS2 63x/1.4 oil
    • EXCITATION
      • 405nm UV laser 50mW
      • White Light Laser, adjustable 470-670 nm, pulsed
    • DETECTION
      • Spectral Confocal Module based on prism with high-sensitivity multiband detection system
      • AOBS beam splitters
      • Two HyD-gated detectors
      • One PMT SP detector
      • One detection channel for transmitted light (DIC)
      • Maximum scanning resolution of 8192x 8192 pixels with a dynamic range of 12 bits per channel
      • Maximum scanning speed of 7 frames/sec, 512X512
      • Maximum scan field: 21.2 mm diagonal
    • STAGE
      • Automated XYZ stage
    • SOFTWARE
      • LAS X acquisition
    Leica SP8X DLS (Digital Light Sheet) and CLSM

  • Olympus BX50: Research microscope for histology

    • OBJECTIVES
      • Olympus PlanApo 2x/0.08
      • Olympus U Plan FL4x/0.13
      • Olympus U Plan FL10x/0.3 Ph1
      • Olympus U plan 20x/0.5 Ph1
      • Olympus PlanApo 40x/0.95 Corr
      • Olympus U plan Fl 40x/0.75 Ph2
      • Olympus ACH 100x/1.25 Oil Iris
    • CONTRAST MODES
      • DIC;Ph1, Ph2
      • Polarization
    • DETECTION
      • PixeLINK colour camera:
        • Maximum resolution: 2043x1536
    • STAGE/STAND
      • Manual stage, tandem view
    • SOFTWARE
      • PixeLINK acquisition software
    OlympusBX50

  • ONI nanoimager super resolution microscopy

    • Applications:
      • PALM, dSTORM, PAINT
      • Extracellular vesicles imaging
    • Exitation: 405, 488, 561, 640 nm laser lines
    • Detection: Emission channels 498-620, 662-710 nm
    • Dichroic split: 640 nm
    • Incubation
      • Temperature control
      • CO2 control
    ONI nanoimager

Spatial-omics microscopy

    • TARGETS
      • a. Human Protein Assays
      • b. Whole Transcriptome Atlas
    • ESCENCE Channels
      • c. Blue-Green:
        • i. Emission wavelength: 516 nm; ± 23 nm
        • ii. Excitation wavelength: 480 nm; ± 28 nm
      • d. Green-Yellow:
        • i. Emission wavelength: 564 nm; ± 15 nm
        • ii. Excitation wavelength: 538 nm; ± 19 nm
      • e. Orange:
        • i. Emission wavelength: 623 nm; ± 30 nm
        • ii. Excitation wavelength: 588 nm; ± 19 nm
      • f. Red:
        • i. Emission wavelength: 683 nm; ± 30 nm
        • ii. Excitation wavelength: 645 nm; ± 19 n

    • 10X Genomics Xenium
    • Spatial transcriptomics at cellular resolution

    • STAND
      • Leica 6000B upright microscope with motorized stage an filter cube change
    • OBJECTIVES
      • 1.25X
      • 6.3X/0.13 UVI
      • 10x/ 0.3 HCXPL Fluotar
      • 20x/ 0.4 HCXPL Fluotar corr
      • 40x/ 0.6 HCXPL Fluotar corr
      • 63x /0.7 HCXPL Fluotar corr
    • FLUORESCENCE FILTERS
      • LMD triple filter
      • Leica A (DAPI)
      • Leica L5 (Green)
      • Leica Y3 9Red)
    • DETECTION
      • LMD cc7000 color camera
      • DMC 300FX color camera
    • STAGE / INCUBATION
      • Automated x,y,z stage. No incubation
    • LASER
      • Crylas cutting laser
      • 50µJ at 355 nm
    • SOFTWARE
      • LAS x acquisition
      • LLM v8.2 Laser Micro Dissection
    Spatial omics microscopy

Image processing and analysis

  • Imaris Workstation

    Software:

    • Imaris 9.6.0 (Oxford Instruments) 3D imaging, including Filament Tracer, Colocalization; Deconvolution
    • ImageJ/FIJI
    • Matlab

    System information:

    • Windows 10
    • Intel® Core ™ i9-10900X CPU @ 3.70 GHz 3.70
    • Cores 10
    • Threads: 20
    • RAM: 128 GB
    • GPU: RTX A4000 16 GB

    Imaris Workstation #2

    Software:

    • Imaris 7.7.2 basic
    • ImageJ/FIJI
    • Velox (Thermo Fisher TEM)
    • MAPS (Thermo Fisher TEM)

    System information:

    • Windows 11
    • Intel® Core ™ i7-6700K CPU @ 4.0 GHz
    • Cores 4
    • Threads: 8
    • RAM: 64 GB
    • GPU: NVIDIA GeForce RTX 2060 6 GB

    Leica Workstation #1

    Software:

    • LASX 3D
    • ImageJ/FIJI
    • Imaris viewer and converter 10.2.0
    • QuPath

    System information:

    • Windows 10
    • Processor: Intel ® Xeon ® W-2223 CPU @ 3.60 GHz 3.60 GH
    • Cores: 4
    • Threads: 8
    • RAM: 64 GB
    • GPU: T1000 4GB

    Leica Workstation #2

    Software:

    • LASX
    • ImageJ/FIJI
    • ONI software
    • Imaris viewer and converter 10.2.0

    System information:

    • Windows 10
    • Processor: Intel ® Xeon ® W-2223 CPU @ 3.60 GHz 3.60 GH
    • Cores: 4
    • Threads: 8
    • RAM: 64 GB
    • GPU: T1000 4GB

    IMOD workstation

    Software:

    • IMOD (TEM tomography reconstruction)
    • ZEN Blue (Zeiss)
    • LASX (Leica)
    • ImageJ/FIJI
    • CellProfiler
    • Ilastik

    System information:

    • Windows 7 or Linux Ubuntu 18.04
    • Processor: Intel ® Xeon ® E5-2680 v4 @ 2.40 GHz 2.40 GHz
    • Cores: 14
    • Threads: 28
    • RAM: 128 GB
    • GPU: Quadro M6000 24 GB

    LightSheet workstation

    Software:

    • ZEN Blue (Zeiss)
    • ImageJ/FIJI

    System information:

    • Windows 10
    • Processor: Intel ® Xeon ® CPU E5-2630 v4 @ 2.20 GHz
    • Cores: 10
    • Threads: 20
    • RAM: 64 GB
    • GPU: Quadro RTX 4000 8GB