The Imaging Unit


The imaging unit provides central light-microscopy-related equipment for the departments of Botany, Genetics and Plant Developmental Biology.


The unit consists of several Olympus instruments including a confocal laser scanning microscope, a widefield fluorescence microscope with deconvolution software, and a high-end fluorescence stereo microscope. The widefield and stereo microscopes are equipped with color (ColorView III) and BW (F-View II) digital cameras. Images are processed on a separate post-acquisition graphics workstation.


The confocal microscope, a FluoView 1000 with an IX81 inverted microscope stand.


Olympus FV1000 pic


If you are curious how it was setup check out this link. A more detailed view of the microscope can be obtained here.



The widefield fluorescence microscope is based on a BX61 upright microscope stand.


The BX61 microscope is equipped with an Optigrid structured illumination setup.


Olympus BX61 pic

Olympus BX61 pic


The reference for structured illumination is Neil 1997 Optics Letters 22:1905-1907 (should you really care...). The QIOPTIQ website details some information about structured illumination and also provides reference literature.


The SZX12 stereo microscope.


Olympus SZX12 pic


The post-acquisition graphics workstation.


A Windows XP Pro (SP2) PC equipped with a 3.2 GHz Intel Pentium 4 processor, 2.0 GB RAM, a RADEON 9800 PRO graphics card, a 185 GB HD, DVD/CD burner, and a Samsung SyncMaster 710N color monitor (1280 x 1024 pixel). We use several software packages for image analysis including Cell^P (2D analysis, made by Soft Imaging and includes blind deconvolution algorithms developed by Autoquant), the Imaris 5.5 suite and Amira (3D analysis), and last but not least the McMaster Biophotonics Facility version of Image J.


Olympus Logo Bitplane Logo
Soft Imaging System Logo Amira Logo


Further Links

A small and obviously incomplete list of molecular plant biology labs using high-end imaging:

Erhardt Lab

Haseloff Lab

The Computable Plant


Advanced microscopy resources on the web:

Advanced Light Microscopy at the EMBL.

Biomedical Imaging Group at the ETH Lausanne. Tutorials and lots of ImageJ plugins.

EAMNET: The European Advanced Light Microscopy Network.
Includes nice teaching modules.

ELMI: The European Light Microscopy Initiative.

PFID: Imaging at the Institut Pasteur in Paris, France. The website includes some very nice seminar videos highlighting many aspects of modern light microscopy.

Wright Cell Imaging Facility at the Toronto Western Research Institute. The facility maintains a special version of ImageJ with numerous plugins. Lots of tips and a really helpfulImageJ manual.


General microscopy resources on the web:

Molecular Expressions Microscopy Primer
Arguably the best knowledge base for all general aspects of light microscopy and digital imaging.
Includes numerous and very helpful interactive java tutorials.

Molecular Probes website
Includes the "The Handbook — A Guide to Fluorescent Probes and Labeling Technologies" and numerous useful resources, such as a fluorescence spectra viewer and various Flash-based tutorials.

Bioimaging Primer of Olympus Biosystems.
Short introduction into basic aspects of modern microscopy.

Optical Highlighters (e.g. PA-GFP, Dronpa, EosFP, Kaede).
Introduction to fluorescent proteins.
Both links include useful information, in particular tables with the properties of the individual fluorescent proteins.

Center of Electron Microscopy at TUM.
Very nice site about electron microscopy. Presently only in German.
The site also represents an excellent knowledge base.

Cytometry Laboratories of Purdue University.
J. Paul Robinson provides a very nice collection of teaching material. For example, check out the BMS524 link.

Roysam site at the Center for Subsurface Sensing and Imaging Systems at Rensselaer Polytechnic Institute.
Check out the very impressive section on cell and tissue image analysis.

Mounts. The site lists recipies and references to many mounting medias
It is provided by by Roy C Ellis, Laboratory Manager, IMVS Division of Pathology, The Queen Elizabeth Hospital, Woodville, South Australia.

Photoshop for Science. The site lists many cool tutorials providing guidance for using Photoshop to generate your images.
The site is run by Jerry (Gerald) Sedgewick, Director of the Biomedical Image Processing Lab at the University of Minnesota.

ImageJ Documentation Portal: Includes a very interesting list of links to image analysis sites.



WWW Virtual Library: Microscopy. A huge directory of all things microscopy.


Financial Support:


The imaging unit was financed through a joint grant (HBFG) provided by the Free State of Bavaria (through the "High-Tech-Offensive, HTO"), the German Ministry of Education and Research, and the German Research Community.



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