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BioImaging facility

The BioImaging Facility provides access to a diverse collection of state-of-the-art imaging systems, including high-end widefield, confocal, and super-resolution microscopes. Our experienced staff with specialised expertise in all stages of the imaging workflow (from experimental design to computational analysis) offers advice and guidance for every step in your imaging project. We provide dedicated application training and courses in light microscopy and image analysis to members and guests of the institute.

Services

  • Setup, daily maintenance and regular quality checks of the microscopes
  • Expert advice on experimental design and sample preparation
  • Microscopy and image analysis training (introductions, workshops, courses)
  • Custom solutions for image processing and quantification
  • Data storage and backup on a central server
  • Small maintenance of microscopes in other departments
  • Technical advice for grant applications and microscopy purchases
  • Access to and assistance with advanced imaging techniques present elsewhere at the NKI, most notably advanced functional and super-resolution imaging techniques (FRET, FLIM, FCS, STORM/PALM, spectroscopy) at the Jalink lab, Multiphoton Intravital Imaging at the van Rheenen lab, Single-molecule dynamics imaging at the Lenstra lab and high throughput/high content screening microscopy at the labs of Beijersbergen and Jalink.

Collaborations outside the Institute

Regular Trainings/Courses

  • Introduction to microscopy : multiple times per year. Designed to give first time users/beginners an overview and theoretical background of basic microscopy techniques.
  • In the footsteps of Antoni van Leeuwenhoek (5-day graduate school basic microscopy course)
  • Basics ImageJ/Fiji course (Image processing & Analyses 2-day course)
  • We regularly (~annually) participate in FEBS- and EMBO-sponsored advanced (functional) imaging courses (organized via LCAM)

Equipment list

Confocal microscopes

  • Zeiss LSM 980 confocal with Airyscan2 (July 2019)
    A point-scanning system on an inverted observer Imager Z.2 microscope with a motorised stage and a variety of objectives (air/oil/water/glycerine), also suitable for DIC. Available laser lines are: 405, 442, 458, 488, 514, 561, 594 and 633 nm. The system has two standard PMT detectors (tuneable), a more sensitive GaAsP spectral detector array and an Airyscan2 detector with fast mode. Incubation chamber for CO2 and temperature-controlled environments.
  • Leica TCS SP8 confocal
    This point-scanning system is based around a fully motorised Leica DM8 inverted microscope equipped with a variety of objectives (air/oil/water) also suitable for DIC. Fluorescence detection is tuneable (400-800nm) with five internal detectors (3x HyD and 2x PMT). Available laser lines are 405, 442, 458, 488, 514, 561, 594 and 633 nm. The scan head has two scanners: conventional (standard) and resonant (fast dynamic). Software licenses for online adaptive deconvolution (Lightning) and Navigator for easy imaging of large regions.
  • Leica SP5 confocal (2x)
    A point-scanning system on an upright DM6000 microscope with fully motorised stage and a variety of objectives (air/oil/water), also suitable for DIC. It has five tuneable fluorescence detectors (3x HyD and 2x PMT). Available laser lines are 405, (442), 458, 476, 488, 496, 514, 561, (594), 633 nm. Incubation chamber for CO2 and temperature-control are present. One systems is equipped with a resonant scanner for fast dynamic imaging.
  • Andor Dragonfly spinning disk confocal
    A spinning disk microscope on an inverted Leica DMI8 microscope with an incubation chamber for temperature and CO2 control. 2 Andor Zyla 4+ sCMOS cameras can be used simultaneously. Capable of bright field, DIC, multi-color fluorescence, z-series, time lapse and multi-stage position imaging. Seven excitation lasers (405, 442, 488, 514, 561, 594 and 637nm). Equiped with TIRF module.

 

Widefield Microscopes

  • Leica TIRF
    Inverted DM6 microscope, equipped with four diode lasers: 405, 488, 561 and 635 nm and an ANDOR iXon Ultra 888 EM-CCD camera. Temperature controlled live cell chamberwith 5% CO2 if necessary. Besides the specific TIRF equipment the system also contains a complete setup for Phase Contrast- and DIC imaging, with objective magnifications in the range 10x to 100x for time-lapse experiments with multichannel fluorescence, Z-stack, multiposition and mosaic imaging.
  • Zeiss Axio Observer Z1 Live (2x)
    A high-quality, inverted, wide-field microscope with motorised stage control (for z sectioning, time lapse, tiling), autofocus and temperature and CO2 control for live cell imaging. Equipped with sensitive Hamamatsu Orca Flash 4 monochrome cameras for bright field, DIC, phase contrast and fluorescence imaging (LED or HXP lightsource). Standard filtercubes are installed (DAPI/CFP/YFP/GFP/mCherry/CY5), more filtersets available on request. 
  • Zeiss Axio Imager Z1 Fixed
    The fully motorized Zeiss AxioObserver Z1 inverted microscope is equipped with a Hamamatsu ORCA AG monochrome cooled CCD-camera for brightfield and phase contrast imaging. Stage inserts allow imaging of cells on glass slides, multiwell plates or dishes up to 10cm. Filter cubes currently installed on the microscope are for DAPI, Alexa488, Alexa568, Cy5 and triple filter cubes excellent for FISH experiments (incl. Blue/SpectumGreen/SpectrumOrange). More filters are avaible on request. Possibility for multiposition, Z-stacks and mosaic tiled images.
  • Zeiss Axiovert 200M Color
    This widefield microscope is suited for high resolution imaging of (immuno-)histochemically stained tissue sections and cells.  The system is equipped with a Zeiss high resolution AxioCam 512 color camera and a motorized x/y scan table. Objectives are available in the range of 1.25x to 100x.  Stage inserts allow imaging of cells on glass slides, multiwell plates or dishes up to 10cm. Possibility to create mosaic images from large tissue samples.
  • Zeiss Axio Scan.Z1 - (Fluorescence) Slide Scanner (July 2019)
    The AxioScan is an automated slide scanner for brightfield and fluorescence microscopy. Up to 100 slides can be loaded and scanned with 10x/0.45, 20x/0.8 or 40x/0.95 objectives. The system creates high-quality virtual slides that can be navigated, zoomed in, etc. Equipped with a sensitive Hamamatsu Orca Flash 4.0 monochrome camera. Multiple fluorescence filtersets available.
  • Zeiss Macroscope
    The Zeiss AxioZoom V16 combines the advantages of a stereomicroscope - zoom optics and long working distance - with the high resolution of a light microscope (NA 0.25). The motorized zoom allows quick and easy switching through the entire 16x zoom range without changing objectives. The macroscope is equipped with both fluorescent and transmitted light. You can view and image large samples (e.g. a complete well of a 12 well plate) with excellent brightness and resolution without the need for tiling and stitching. In addition, the long working distance allows for dissection of small tissue samples.

Workstations
Three high-end workstations with image processing & analysis software (Huygens, Imaris, Matlab, Leica Las X en Zeiss Zen, Cell profiler, FIJI/ImageJ)

Selected Publications

  • Dijkgraaf FE, Matos TR, Hoogenboezem M, Toebes M, Vredevoogd DW, Mertz Mvan den Broek B, Song JY, Teunissen MBM, Luiten RM, Beltman JB & Schumacher TN Tissue patrol by resident memory CD8 T cells in human skin. Nature Immunology, 2019. doi: 10.1038/s41590-019-0404-3
  • Xu G, Chapman JR, Brandsma I, Yuan J, Mistrik M, Bouwman P, Bartkova J, Gogola E, Warmerdam D, Barazas M, Jaspers JE, Watanabe K, Pieterse M, Kersbergen A, Sol  W, Celie PHN, Schouten PC, van den Broek B, Salman A, Nieuwland M, de Rink I, de  Ronde J, Jalink K, Boulton SJ, Chen J, van Gent DC, Bartek J, Jonkers J, Borst P, Rottenberg S. REV7 counteracts DNA double-strand break resection and affects PARPinhibition. Nature. 2015 May 28;521(7553):541-544. doi: 10.1038/nature14328. Epub 2015 Mar 23.
  • Feringa FM, Krenning L, Koch A, van den Berg J, van den Broek B, Jalink K, Medema RH. Hypersensitivity to DNA damage in antephase as a safeguard for genome stability. Nature Communications 2016 Aug 26;7:12618. doi: 0.1038/ncomms12618.
  • Oomen L, Sacher R, Brocks H, Zwier J, Brakenhoff G, Jalink K. Immersion oil for high-resolution live-cell imaging at 37°C: optical and physical characteristics. J Microsc. 2008; 232: 353-61.
  • Zwier J, Oomen L, Brocks H, Jalink K, Brakenhoff G. Quantitative image correction and calibration for confocal fluorescence microscopy using thin reference layers and SIPchart-based calibration procedures. J Microsc. 2008; 231: 59-69.

Publications

  • Oomen L, Sacher R, Brocks H, Zwier J, Brakenhoff G, Jalink K. Immersion oil for high-resolution live-cell imaging at 37°C: optical and physical characteristics. J Microsc. 2008; 232: 353-61.
  • Zwier J, Oomen L, Brocks H, Jalink K, Brakenhoff G. Quantitative image correction and calibration for confocal fluorescence microscopy using thin reference layers and SIPchart-based calibration procedures. J Microsc. 2008; 231: 59-69. 
  • Brakenhoff GJ, Wurpel GW, Jalink K, Oomen L, Brocks L, Zwier JM. Characterization of sectioning fluorescence microscopy with thin uniform fluorescent layers: Sectioned Imaging Property or SIPcharts. J Microsc. 2005; 219: 122-32.

People working at the BioImaging facility

Brocks, Lenny.jpg

Lenny Brocks

Facility manager BioImaging facility

Personal details

Experience

  • Setup and maintenance of the microscope systems by a daily basic check-up and regular tests for more hidden possible malfunctioning
  • Make proposals for investments, based on user needs and developments in the field
  • Introducing users to the basics of microscopy and teach them how to use the specific system(s)
  • Help and advise in using the microscopes and sample imaging. In addition for each system an extensive user manual is made
  • Take care of storage and archiving by making backups of all data acquired on the microscopes
  • Provide help in image enhancement and processing

 

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Broek, Bram van den.jpg

Bram van den Broek

Postdoctoral fellow (Operator high-content confocal screening microscope)

Experience

I am a physicist who has specialized in single-molecule biophysics (PhD) and cellular biophysics (postdoc), with an emphasis on microscopy technique development (including optical tweezers, multifocal 2-photon microscopy, 3D tracking).
 
At the NKI I have a supportive role. In the Jalink lab I focus on developing and maintaining various advanced microscopy and related techniques. Additionally I construct image analysis tools that aid cell biologists to quantify and interpret their data.
 
I am also the contact person for high-resolution confocal high-content screening at the NKI. And I' am working as Operator high-content confocal screening microscope.

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Marjolein Mertz

Marjolijn Mertz

Facility manager, BioImaging facility

Personal details

Experience

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