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Imaging Core Facility at the Biozentrum

During the past two decades 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, now also in combination with artificial intelligence, 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 core 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).

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 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 800 inverted
  • Zeiss LSM 880 inverted with incubation chamber for live cell imaging and Airyscan FAST

Spinning Disk Confocal Microscopes:

  • Olympus SpinSR with dual camera setup for high speed live-cell imaging and Olympus Super Resolution (OSR)
  • Olympus SpinD with dual camera setup for high speed imaging

Wide-field live cell imaging systems:

  • Cytiva DeltaVision system
  • FEI MORE system with TIRF

Standard wide-field system:

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

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:

  • Cytiva 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 image analysis:

  • Python / SciPy / NumPy
  • Matlab
  • CellProfiler
  • In-house plugin or macro development for specific image analysis solutions (please come to our Wednesday Workshop to discuss the details)

Area of responsibility:
The IMCF's area of responsibility covers exclusively microscopy and IT infrastructure systems of the Imaging Core Facility. These facility systems are supervised and maintained by IMCF-staff and must be booked via the PPMS online booking system.

The IMCF is NOT responsible for microscopes of Biozentrum research groups. IMCF staff are available to advise Biozentrum scientists on the selection of new systems. Maintenance, setup, upgrades, repairs, alignments, cleaning or introductions to group microscopes will NOT be carried out by the IMCF.

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.

Light sheet microscopy of cleared large samples as well as deep learning in image analysis are the main fields of development in the years ahead. IMCF will continue to watch the market, evaluate new systems and try to be among the first to implement new microscopy and image analysis technologies at the Biozentrum.

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