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UMCG Microscopy and Imaging Center (UMIC)

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

UMIC is a DTL Hotel, i.e. a Dutch Techcentre for Life sciences, and an nPOD core facility and, therefore, participates in the Network for Pancreatic Organ Donors with Diabetes.

We participate in Netherlands microscopy gateway.

Get started at UMIC

A training session of about 1,5 hour for each instrument and a registration as UMIC user is mandatory.

  • Before you can use any of the microscopes unsupervised, you have to undergo individual training. This training will be provided by assigned instructors; training by other parties is not allowed. Each microscope requires its own specific training. It is not permitted to use equipment without prior training or booking.

    • Please contact us to make an appointment for an individual training;
    • After you have completed the training and registration, you will get access to the facilities and the Booked Scheduler reservation system.
  • If you have successfully completed the training, you can register as a UMIC user. We will then give you access to the agenda and authorize you to book the equipment you need. This takes about 1 or 2 working day(s);

  • Reservations

    • Reservations can be made up to two weeks ahead and for no more than four hours a day;
    • Experienced users can also make reservations for longer periods of time, i.e. during weekends, evening hours, and holidays;
    • Reservations for specific activities, such as courses or handling patient materials, must be discussed with us;
    • There are no booking restrictions for the IncuCytes.

    Cancellations

    • If applicable, reservations must be cancelled 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 decide to assign the instrument to another user.
  • Learn more about UMIC rules and fees.

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.
    • 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.
    • 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).

All EM sample preparations, including HPF/FS/vibrating microtome

    • 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, sample carriers with a depth of 100 to 300 µm, and tubing;
    • EM AFS2 Freeze substitution (Leica)
    • The EM AFS2 is an automatic freeze substitution system used for the resin embedding of biological samples following high pressure freezing;
    • (Cryo-) Ultramicrotome 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 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 SCD050 (Leica)
    • The SCD050 can be used to sputter coat samples for SEM with gold/palladium and, therefore, make them conductive.
    • The film thickness can be monitored with a quartz thickness monitor.
    • Carbon coating of samples or formvar grids (in order to make them hydrophilic) is also possible.
    • Leica Tissue Processor
    • For fully automated and semi-automated resin embedding of EM samples.

(Confocal microscopy) for live cells/tissues

    • Specifications Zeiss LSM 780 NLO
    • STAND
      • Zeiss Axio Observer Z1 (inverted).
    • OBJECTIVES
      • Plan-Apochromat 10x/0.45 (WD=2.1 mm);
      • Plan-Apochromat 20x/0.8 (WD=0.55 mm);
      • Plan-Neofluar 40x/1.30 Oil DIC (WD=0.21 mm);
      • C-Apochromat 40x/1.2 W Corr UV-VIS-IR (WD=0.28 mm);
      • Plan-Neofluar 63x/1.3 Imm Corr DIC for water or glycerine immersion;
      • Plan-Apochromat 63x/1.40 Oil DIC (WD=0.19 mm).
    • EXCITATION
      • 405, 440, 458, 488, 514, 561,594, 633 nm laser lines;
      • 2 Photon: 680-1080 nm tunable;
      • 2 Photon OPO: 1000-1280 nm tunable.
    • DETECTION
      • 34-channel 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 simultaneously, 4 tracks sequentially;
      • It is possible to perform FCS and FCCS using the Quasar detector.
    • STAGE/INCUBATION
      • Incubator XL DARK S1 (temperature and CO2 control);
      • Heating Insert for 3 cm 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 scan field diagonal;
      • Tiling, z-stack, positions, and time lapse are possible in different combinations.
    • SOFTWARE
      • ZEN black acquisition;
      • FCS/ FCCS;
      • Colocalization;
      • 3D;
      • Spectral unmixing;
      • Tile scan.
    • This system has a coupling with one Chameleon Vision compact OPO two-photon laser together with an upright LSM7 MP.
    • Specifications 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.
    • Specifications 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 DMI 8CS DLS inverted microscope with fully-motorized objective nosepiece, 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 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/INCUBATION
      • Automated XYZ stage. No incubation available yet.
    • SOFTWARE
      • LAS X acquisition.
    • 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
    • Specifications 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

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.
    • 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

    • Specifications 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.
    • Specifications 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.
    • Specifications 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) microscopy for fixed cells and tissue

    • Specifications TissueFaxs microscope
    • STAND
      • Zeiss Axio Observer 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 for FRET;
      • Zeiss filter set 46 YFP shift-free for FRET;
      • Zeiss filter set 48 CFP/YFP shift-free for FRET;
      • Zeiss Bleach Set 01 YFP for 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
      • Temperature, CO2- and O2-controlled environment via Pecon Lab-Tek insert;
      • Ultraprecise automated Märzhäuser object table;
      • Inserts for 12 separate slides or one multiwell (6- or 96-well) plate;
      • Pre-programmed for TMA analysis.
    • SOFTWARE
      • TissueFaxs acquisition software;
      • TissueQuest fluorescence analysis software (on a separate workstation);
      • HistoQuest histology analysis software (on a 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 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.
    • 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
      • 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.
    • Specifications 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.

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
  • Specifications will follow

    • 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

  • Computer 1

    • Imaris 9.6.0  (Oxford Instruments) 3D imaging, including Filament Tracer, Colocalization; Deconvolution
    • IMOD (freeware) EM tomography;
    • CellProfiler (freeware) high-content analysis
    • MatLab
    • FIJI

    Computer 2

    • Imaris 7.6.5 basic;
    • Huygens professional 4.0 (SVI) 3D Deconvolution and colocalization;
    • HistoQuest (TissueGnostics) Image quantification brightfield images;
    • TissueQuest (TissueGnostics) Image quantification fluorescent images;
    • ZEN Black and ZEN Blue (Zeiss);
    • CellProfiler (freeware) high-content analysis.
    • FIJI

    Computer 3

    • LAS X 3D (Leica);
    • FIJI
    • Cellprofiler

    Computer 4

    • IMOD (tomography reconstructions)
    • FIJI
    • Cellprofiler
    • ZEN Black and ZEN Blue (Zeiss)

    Computer 5

    • Data uploading to Omero only

    Computer 6

    • Lightsheet data analysis

    Computer 7 & 8

    • Incucyte acquisition and analysis