Microscopy & Imaging Center - UMIC

Microscopy infrastructure to support state of the art research in medical and biological sciences. Facility
UMIC offers training and access to advanced microscopes and image processing to external users and researchers of the UMCG or the RUG.
Relevance

Integral part of the Dutch microscopy landscape

We participate in:

NEMI is DTL-hotel, a Dutch techcentre for life sciences and also a nPOD-facility, and thus a partner in the Network for Pancreatic Organ Donors with Diabetes.

Booking information

Before you can work independently on any of the microscopes

  • Before you can work independently on any of the microscopes, you have to follow an individual training.

    • Please contact the manager for an appointment.
    • The training will be provided by assigned instructors.
    • Training by other parties does not count.
    • After training and registration, the manager will provide you access to the facilities and to the reservation system: Bookedscheduler.
    • You'll need a separate training for every microscope. It is not permitted to use equipment without training or booking.
  • Create a personal account simply by clicking the “create an account” link on the front page of Bookedscheduler:

    • Fill in a form, your e-mail, first- and last name are obligatory, your phone number can be useful, other people can call you when equipment is available for instance
    • After you submit this form, it will take one working day for the managers to give you access to the agenda and authorize you to book the equipment you need.
    • Your time slots will be used for fee calculations.
    • Please change slots according to the time you actually used the equipment. This can be done as long as the time slot is not expired.
    • Only the managers can change expired slots.
  • Reservations

    • Reservations can be made up till two weeks ahead and no more than four hours a day.
    • Exceptions are reservations made for educational purposes or guests.
    • Weekends, evening hours, and holidays can also be reserved by experienced users for longer periods.
    • Other special circumstances for reservations further ahead in time, such as the use of patient-material, have to be discussed with the manager.
    • The Solamere and the SP2 do not have any restrictions on booking.

    Cancellations

    • If reservations need to be canceled, you have to undo your reservation in the booking system.
    • If possible notify the next user. This can be done easily by clicking on the name of a reservation. An extra window will appear showing you the e-mail address.
    • No-shows may be charged the hourly fee!
    • Half hour or more too late, the instrument can be assigned by the manager to another user.
  • After training and your account being authorized by a manager, book all equipment online in Bookedscheduler.

Electron Microscopy, Nanotomy & ColorEM

    • CM100-bio (FEI) Transmission Electron Microscope
    • Tungsten electron source.
    • Acceleration voltage: 40 to 100 kV (aligned for 80 kV).
    • Goniometer: 4-axis, fully motorized stage.
    • Side-mounted Morada Camera (CCD, 11 megapixels) with Soft Imaging Solutions acquisition software.
    • ​​​​Supra 55 Scanning Electron Microscope (Zeiss)
    • For specifications see Brochure Zeiss Supra Series
    • 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)
    • Color EM by using EDX detection in Life Sciences
    • 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 symmetrical positioned Dual Bruker XFlash6 100mm2 EDS detectors for sensitive elemental detection
    • Software and hardware for 3D tomography acquisition of TEM images but also for 3D EDS images
    • MAPS software for mosaic large area acquisition
    • Company page
    • EDX detector X-max 150 (Oxford Instruments)
    • A 150 mm2 Silicon Drift Detector mounted on the Zeiss Supra 55 gives enough sensitivity to be used not only in material sciences, but also in life sciences.
    • For specifications see Brochure Xmax150
    • ATLAS 5 Large Area Imaging (Zeiss/Fibics)
    • An external scan generator connected to the Zeiss Supra55 SEM can record multiple tiles up to 32k x 32k pixels automatically. These tiles can be stitched yielding very big fields of view (millimeters) with nm resolution.
    • Sample holders are available enabling multi-sample imaging of up to 11 TEM grids or 9 SEM samples.
    • Data are stored on a LAN network, connected with two offline PCs where these acquired data are stitched and exported either as Big-TIF or as a HTML file, which will be put on our server.
    • For more information see this page.
    • SECOM (Delmic)
    • A light microscope that can be put in the Supra55 SEM by replacing the door of the vacuum chamber
    • This enables simultaneous photon detection and electron detection (SE2 or In-Lens BSD)
    • For specifications see this page.
    • Applications in CLEM (Correlative Light and Electron Microscopy) and Cathode Luminescence

All EM Sample prep, including HPF/FS/vibra- micro-tome

    • EM-ICE High Pressure Freezer (Leica)
    • High Pressure Freezing of biological samples in combination with light stimulation can be performed using different sample carriers such as sapphire discs, 100 – 300 µm deep sample carriers, tubing.
    • For more detailed information see this page.
    • EM AFS2 Freeze substitution (Leica)
    • After High Pressure Freezing of biological samples can be embedded in resin by freeze substitution using the AFS2.
    • For more detailed information see this page.
    • (Cryo-) Ultramicrotomes UC7/FC7 (Leica)
    • Two room temperature ultramicrotomes and one cryo ultramicrotome are available for cutting semi thin and ultra-thin sections.
    • For training purposes a camera plus TV screen can be mounted
    • See page.
    • Milling Device EM-Rapid (Leica)
    • For fast milling of plastic embedded samples a EM-Rapid (Leica) milling device is available.
    • See page.
    • Leica VT1000S Vibratome
    • This vibratome can cut sections from 1 µm up to 999 µm
    • Applications:
      • Brain research
      • Tissue slice cultures
      • Immunolabeling
      • EM sample preparation
    • Sputter coater SCD050 (Leica)
    • With the SCD050 samples for SEM can be sputter coated with Palladium/Gold to make them conductive.
    • Thickness can be monitored with a quartz thickness monitor.
    • Also carbon coating of samples or formvar coated grids (to make these hydrophilic) is possible.
    • Leica Tissue Processor
    • For (semi) automated resin embedding of EM samples

Confocal microscopy for live cells/tissues

    • Specifications LSM Zeiss 780 NLO
    • STAND
      • Zeiss Axio Observer Z1 (inverted)
    • OBJECTIVES
      • “PlanApochromat" 10x/0.45 (WD=2.1mm)
      • "PlanApochromat" 20x/0.8 (WD=0.55mm)
      • “Plan Neofluar"40x/1.30OilDIC (WD=0.21mm)
      • "C Apochromat"40x/1.2WCorr UVVISIR (WD=0.28mm)
      • "PlanNeofluar" 63x/1.3Imm CorrDIC water or glycerine immersion
      • "PlanApochromat" 63x/1.40 Oil DIC (WD=0.19mm)
    • EXCITATION
      • 405, 440, 458, 488, 514, 561,594, 633 nm laser lines
      • 2Photon: 680-1080 nm tunable
      • 2 Photon OPO: 1000-1280 nm tunable
    • DETECTION
      • 34channel Quasar detector (32 GaAsP element array and 2 side PMTs)
      • External detection module BiG DIC/transmitted, (forward), 2 channels
      • External detection module BiG incident light (backwards), 2 channels
      • BiG filters: 380-430/470-515, 420-475/500-550, 455-500/575-610, 500-550/575-610, 525-560/650-750
      • Spectral imaging
      • Up to 10 channels simultaneous, 4 tracks sequential
      • FCS or FCCS possible on Quasar detector
    • STAGE / INCUBATION
      • Incubator XL S1 DARK (temp. and CO2 controlled)
      • Heating Insert for 3cm petri dishes
      • Heatable universal plate mounting frame
      • Universal mounting frame
      • Scan speed up to 250 frames/sec (512x16 pixels, high mag)
      • Scan resolution up to 6144x6144 pixels
      • 20 mm scanfield diagonal
      • Tiling, z-stack, positions, time lapse in different combinations possible
    • SOFTWARE
      • ZEN black acquisition
      • FCS/ FCCS
      • Co-localization
      • 3D
      • Spectral unmixing
      • Tile scan
    • This system has coupling with one Chameleon Vision compact OPO two photon laser together with upright LSM7 MP .
    • Specifications Zeiss LSM 7 MP
    • STAND
      • Zeiss Axio Examiner (upright)
    • OBJECTIVES
      • "Plan Neofluar" 5x/0.16 M27 (WD=18.5mm)
      • W “Plan Apochromat" 20x/1.0 DIC (WD=1.8mm), (UV) VIS IR
      • W "Plan Apochromat" 40x/1.0 DIC (WD=2.5mm), VIS IR
      • "C Achroplan" 32x/0.85 W Corr VIS IR, (WD=1.1mm at D=0.17mm) (D=0 - 0.17mm)
    • EXCITATION
      • 2Photon: 680-1080 nm tunable
      • OPO 2Photon: 1000-1280 nm tunable
      • Wide-field fluorescence 3 channels
    • DETECTION
      • External detection module BiG incident light (reflection) 2 channels
      • External detection module PMT DC/transmitted 2 channels
      • Camera: AxioCam MRm Rev. (1.4 Mega pixel Pixel size: 6.45 um x 6.45 um)
    • STAGE / INCUBATION
      • Incubator XL S1 DARK (temp controlled)
      • Universal mounting frame
      • Tiling, z-stack, positions, timelapse in different combinations possible
      • Adapted for intra-vital imaging
    • SOFTWARE
      • ZEN black, 3D rendering included
    • Specifications Zeiss Cell Discoverer 7
    • STAND
      • Zeiss Cell Discoverer high content microscope with LSM900 confocal head
    • OBJECTIVES
      • PlanApochromat 5x/0.12 (WD=5.1mm)
      • PlanApochromat 20x/0.35-0.8 (WD=2.2mm) Autocorrection*
      • PlanApochromat 50x/1.2 water (WD=0.84mm) Auto correction* and auto 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 Airyscan2 detector, fast, high s/n ration and (Super) high resolution
        • 2 PMT detectors
      • Wide field:
        • 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 2x incubation boxes
      • Insert for 2 microscopy slides
      • Temperature controlled
      • CO2 and O2 levels controlled
      • Software and hardware (definite) autofocus
      • Tiling, z-stack, positions, time lapse in different combinations possible
    • SOFTWARE
      • ZEN blue acquisition, image analysis
      • Cell Profiler analysis
    • This system has coupling with a ThermoFisher Cytomat incubator for 42 plates via a PAA robot.
    • Specifications Leica SP8X DLS confocal/light sheet
    • STAND
    • Leica DMI 8CS DLS Inverted microscope with fully motorized objective nosepiece and fluorescence filter cube change and Digital Light Sheet option.
    • 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 beamsplitters
      • 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 per second, 512X512.
      • Scanfield max: 21,2 mm diagonal.
    • LIGHTSHEET
      • Detection objectives: 25x, 10x,
      • Illumination objective: 5x, 2.5x
      • DFC9000 GTC DLS sCMOS camera (up tp 70 fps, 2048 x 2048)
    • STAGE / INCUBATION
      • Automated x,y,z stage. No incubation yet
    • SOFTWARE
      • LAS X acquisition
    • Specifications DeltaVision Elite
    • STAND Inverted Olympus IX-71 Stand
    • OBJECTIVES
      • PLAPON 60X oil, 1.42, WD 0.15 mm. (Olympus)
      • UPFLN 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 colors DV light SSI (Lumencore ultra-fast 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; pixelsize 6.5 um x 6.5 um, 2560 x 2160 pixels,
      • Speed: 400 fps at 512 x 512, 200 fps at 1025 x 1025
    • STAGE / INCUBATION
      • Environmental chamber, temp and CO2 control
      • Ultimate focus module
      • Automated Flexure stage
      • Live cell speed option: enables multi-color imaging without filter change.
    • SOFTWARE
      • softWoRx 6 aquisition and integrated deconvolution software (on Linux CentOS 6.3 platform)
      • Working station with one 30'' monitor

High content (confocal) fluorescence microscopy for live cells

    • Specifications Zeiss Cell Discoverer 7
    • STAND
      • Zeiss Cell Discoverer high content microscope with LSM900 confocal head
    • OBJECTIVES
      • PlanApochromat 5x/0.12 (WD=5.1mm)
      • PlanApochromat 20x/0.35-0.8 (WD=2.2mm) Autocorrection*
      • PlanApochromat 50x/1.2 water (WD=0.84mm) Auto correction* and auto 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 Airyscan2 detector, fast, high s/n ration and (Super) high resolution
        • 2 PMT detectors
      • Wide field:
        • 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 2x incubation boxes
      • Insert for 2 microscopy slides
      • Temperature controlled
      • CO2 and O2 levels controlled
      • Software and hardware (definite) autofocus
      • Tiling, z-stack, positions, time lapse in different combinations possible
    • SOFTWARE
      • ZEN blue acquisition, image analysis
      • Cell Profiler analysis
    • This system has coupling with a ThermoFisher Cytomat incubator for 42 plates via a PAA robot.
    • Specifications IncuCyte S3 Live-Cell Analysis System
    • For easy imaging and analyzing live cells over days to months inside an incubator
    • OBJECTIVES
      • 20x
        • Image Resolution: 0.62 microns/pixel
        • Image Size: 1408 x 1040 pixels
        • Field of View: 0.88 x 0.65 mm
      • 10x
        • Image Resolution: 1.24 microns/pixel
        • Image Size: 1408 x 1040 pixels
        • Field of View: 1.75 x 1.29 mm
      • 4x
        • Image Resolution: 2.82 microns/pixel
        • Image Size: 1536 x 1152 pixels
        • Field of View: 4.34 x 3.25 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
      • Temp, CO2 controlled environment, whole instrument is installed inside a Panasonic MCO-230AIC incubator
      • Stage can hold six multiwell plates at the same time. The stage is fixed, a microscope unit is travelling underneath it for scanning (parts of) the wells. 2d only.
    • SOFTWARE
      • The IncuCyte can be controlled from any networked location using unlimited, free licenses to be obtained at UMIC
      • Basic analysis software included
    • Specifications IncuCyte ZOOM Live-Cell Analysis System
    • For easy imaging and analyzing live cells over days to months inside an incubator
    • OBJECTIVES
    • (Only one objective in the instrument, can be changed upon request)
      • 20x: Image Resolution: 0.61 microns/pixel
      • 10x: Image Resolution: 1.22 microns/pixel (standard)
    • FLUORESCENCE FILTERS
      • Green
        • Excitation Wavelength: 460 nm; Passband: [440,480] nm
        • Emission Wavelength: 524 nm; Passband: [504,544] nm
      • Red
        • Excitation Wavelength: 585 nm; Passband: [565,605] nm
        • Emission Wavelength: 635 nm; Passband: [625,705] nm
    • BRIGHTFIELD
      • HD Phase imaging in grey values
    • DETECTION
      • Camera Type: Basler Sca 1329x1040 px 12 bit
      • Sensor Type: Sony ICX285 CCD
    • STAGE / INCUBATION
      • Temp, CO2 controlled environment, whole instrument is installed inside a Panasonic MCO-230AIC incubator
      • Stage can hold six multi well plates at the same time. The stage is fixed, a microscope unit is travelling underneath it for scanning (parts of) the wells. 2d only.
    • SOFTWARE
      • The IncuCyte can be controlled from any networked location using unlimited, free licenses to be obtained at UMIC
      • Basic analysis software included

(Confocal/fluorescence) microscopy for fixed cells

    • Specifications Tissuefaxs microscope
    • STAND: Zeiss AxioObserver Z1
    • OBJECTIVES
      • Zeiss- EC “Plan-Neofluar” 2.5x/0.075 Dry
      • Zeiss- EC "Plan-Neofluar" 10x/0,3 Dry, Ph1
      • Zeiss- LD "Plan-Neofluar" 20x/0,4 Corr Dry, Ph2
      • Zeiss- EC "Plan-Neofluar" 40x/1,30 Oil, DIC
      • Zeiss- "Plan-Apochromat" 63x/1,40 Oil, DIC
      • Zeiss –LD “Plan-Neofluar” 40x /0,6 DIC
    • FILTER SETS
      • Zeiss-filter set 47 CFP shift free voor FRET
      • Zeiss-filter set 46 YFP shift free voor FRET
      • Zeiss-filter set 48 CFP/YFP shift free voor FRET
      • Zeiss Bleach Set 01 YFP voor FRET
      • Chroma ET Dapi-filter set
      • Chroma ET FITC/GFP-filter set
      • Chroma ET CY3-filter set
      • Chroma ET Cy5-filter set
      • Chroma Far infrared filter IR Dye 800
    • DETECTION
      • Monochrome camera system PCO Pixelfly II 1.4 Megapixels
      • CMOS-color camera PL-B623 Pixelink 3.1 Megapixels
    • STAGE / INCUBATION
      • Temp, CO2, O2 controlled environment via Pecon Lab-Tek insert
      • ultra precise automated Märzhäuser object table
      • inserts for 12 separate slides or one multi (6 or 96) well plate
      • pre-programmed for TMA analysis
    • SOFTWARE
      • TissueFaxs acquisition software
      • TissueQuest fluorescence analysis software (on separate workstation)
      • HistoQuest histology analysis software (on separate workstation)
    • Specifications 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 beamsplitters
      • Two confocal detection channels for reflection and fluorescence with tunable band-width and central wavelength in continuous and independent form for each channel.
      • 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 per second, 512X512.
      • Scanfield max: 21,2 mm diagonal.
    • STAGE / INCUBATION
      • Automated x,y,z stage. No incubation
    • SOFTWARE
      • LAS X aquisition
    • Specifications 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
      • EL 6000 lightsource
      • Filters
        • LPA (DAPI)
        • L5 (Gfp-FITC)
        • TXR (Texas Red)
        • Y3 (Cy3)
        • Y5 (Cy5)
    • DETECTION
      • Leica DFC3000 G camera
    • STAGE / INCUBATION
      • Manual x,y,z stage. No incubation
    • SOFTWARE
      • Leica LAS 4.3 acquisition
    • Specifications Olympus BX50: Research microscope for histology
    • OBJECTIVES
      • Olympus PlanApo 2x/0.08
      • Olympus UPlan FL4x/0.13
      • Olympus Uplan FL10x/0.3 Ph1
      • Olympus Uplan 20X/0.5 Ph1
      • Olympus PlanApo 40x/0.95 Corr
      • Olympus Uplan Fl 40x/0.75 Ph2
      • Olympus Ach 100x/1.25 Oil Iris
    • CONTRAST MODES
      • DIC
      • Ph1, Ph2
      • Polarization
    • DETECTION
      • PixeLINK color camera
        • Max resolution 2043x1536
    • STAGE / STAND
      • Manual stage, Tandem view
    • SOFTWARE
      • PixeLINK acquisition software

Image processing & analysis

  • Room 1

    • Imaris 7.6.5 basic
    • Huygens professional 4.0 (SVI) Deconvolution 3d and coloc
    • Histo Quest (Tissuegnostics) Image quantification brightfield images
    • Tissue Quest (Tissuegnostics) Image quantification fluorescent images
    • ZEN Black and ZEN Blue (Zeiss)
    • Cell Profiler(freeware) high content analysis

    Room 3

    • Imaris 7.6.5 (Oxford Instruments)- 3D imaging including Filament Tracer and coloc
    • LASX 3D (Leica)
    • IMOD (freeware) EM tomography
    • Cell Profiler(freeware) high content analysis