Dr. Oliver Biehlmaier

Biozentrum
University of Basel
Klingelbergstrasse 50 / 70
CH - 4056 Basel
Kragenbau, Room G1054 Phone: +41 61 207 20 73
Email: oliver.biehlmaier-at-unibas.ch
Curriculum Vitae

Imaging Core Facility (IMCF)

Imaging Core Facility at the Biozentrum

Fig. 1: Overview of the systems and activities of the Imaging Core Facility (Word cloud created with wordle.net).

During the past decade the importance of light microscopy increased tremendously in all types of biological research. In addition to the image acquisition at various types of microscopes, data handling and image analysis is becoming more and more important.

Microscopes and support for image analysis is available for all research groups of the Biozentrum

The Imaging Core Facility (IMCF) provides infrastructure for all microscopy techniques currently used in life sciences. The microscopes in the facility span the entire range from standard wide-field microscopy to confocal microscopy and super-resolution microscopy. The newly established facility started to operate in autumn 2011. There are 6 point scanning confocal microscopes, 2 spinning disk confocal microscopes, 3 wide-field microscopes, a serial 2-Photon tomography microscope, a lightsheet microscope, a slide scanner and a 3D-SIM super-resolution microscope available. The aim of the IMCF is not only to provide the facility users with well-maintained modern microscopy systems as well as with theoretical and technical support but also to develop and adapt new microscopy techniques and image analysis routines.

Areas of interest

Besides the microscopy service for the Biozentrum, research at the IMCF focuses on the development of (i) optimal system performance in terms of image acquisition speed and experimental flexibility thereby enabling users to do all types of experiments under optimal conditions, (ii) image analysis and automation solutions, and (iii) a data storage and database solution (in collaboration with Research IT).

Fig. 2: Zeiss LSM700 inverted scanning confocal with incubation chamber for live imaging, large samples, and FRAP.

Areas of activity

The IMCF supports projects requiring specific light and fluorescence microscopy setups. Preferably, the IMCF should be involved at every stage: in the planning of a new imaging / microscopy project (selection of fluorescent dyes, choice of microscopy system), during the initial phase (helping with the actual experimental setup including the soft- and hardware settings), and in image analysis and quantification (advice on usage of image analysis software such as Icy, Arivis, Imaris and Fiji/ImageJ). Only this allows the IMCF to provide the best support at all stages of the project and to adapt the experimental settings to the specific needs.

 

We also provide a weekly open support (every Wednesday morning), where users can come and discuss their issues with members of the IMCF, without having to take an appointment (details).

Specific services and resources

In detail, we will provide the following state of the art microscopy systems for research groups:

Point Scanning Confocal Microscopes:

  • Inverted Leica SP5 I system with resonance scanner for fast scanning (live cell imaging), multiphoton laser, and incubation chamber.
  • Inverted Leica SP5 II system with resonance scanner for fast scanning (live cell imaging), high sensitivity HyD-detectors, Matrix screening software, and incubation chamber.
  • Inverted Leica SP8 system with resonance scanner for fast scanning (live cell imaging), and incubation chamber. !BSL2 system!
  • Zeiss LSM 700 upright
  • Zeiss LSM 700 inverted
  • Zeiss LSM 800 inverted with incubation chamber for live cell imaging and Airyscan

Spinning Disk Confocal Microscopes:

  • PerkinElmer Ultraview with dual camera setup for high speed imaging
  • 3i Spinning Disk with highly sensitive Photometrics Evolve EM-CCD camera

Wide-field live cell imaging systems:

  • Applied Precision DeltaVision system
  • FEI MORE system with TIRF

Standard wide-field system:

  • Leica DM 6000, upright microscope with color camera for histology images

Serial 2-photon Tomography system:

  • TissueVision TissueCyte, to image whole organ imaging at high resolution without clearing procedures

Lightsheet system:

  • Zeiss Z1 lightsheet, for live & fixed large samples

Slide scanner system:

  • Zeiss Axio Scan.Z1, fully automated for high throughput

Super-resolution 3D-SIM system:

  • GE Heathcare OMX v4 Blaze, for fixed and live samples, with structured illumination (3D-SIM), Ring TIRF (works with PALM or TIRF techniques)

 

Data visualization and image analysis software:

For 3D-rendering, tracking, and animations of microscopy data:

     

    • Arivis
    • Icy
    • Imaris
    • Volocity
    • FiJi / ImageJ

     

For reconstruction of 3D multi-position stacks (registration, stitching):

     

    • XuvTools

For image analysis:

     

    • Python / SciPy / NumPy
    • Matlab
    • CellProfiler
    • In-house plugin or macro development for specific image analysis solutions

     

Steering committee

To coordinate the Imaging Core Facility activities at the Biozentrum a steering committee has been established in 2011. The steering committee is composed of five group leaders from different focal areas of the Biozentrum that are heavily involved in microscopy, and representatives from Research IT and from the Biozentrum coordination office.

Outlook

Light microscopy is developing at a tremendous pace and several new microscopy techniques have been developed to bypass Abbé’s diffraction limit of light. These new super resolution technologies are either based on structured illumination, nonlinear fluorophore responses, or on the precise localization of single molecules. Depending on the type of method used, it is now possible to improve the maximal resolution from 200nm to values of 50 to 100nm.

After careful evaluation of the different techniques, the IMCF of the Biozentrum is planning to provide super-resolution techniques at the facility. Super-resolution microscopy will open up a new dimension for research at the cellular and subcellular level. Hitherto non-resolvable small subcellular structures such as centrioles, lipid rafts, neuronal dendrite spines, nuclear pore complexes, bacterial polar complexes, and many other macromolecular structures with less than 200nm in diameter - so far exclusively accessible by electron microscopy - will be visualized by light microscopy, and eventually live cell imaging.