About Imaging Facility

MPI of Immunobiology and Epigenetics

About MPI of Immunobiology and Epigenetics

The Max Planck Institute of Immunobiology and Epigenetics (MPI-IE) in Freiburg is an interdisciplinary research institution that conducts basic research in two key areas of modern biology. Immunobiology is concerned with the ways multicellular organisms defend themselves against pathogens. An international team of scientists studies the evolutionary origins and the development of lymphoid organs and immune effector cells, the function of antigen receptors, and the genetic basis of host-pathogen interactions. Epigenetic research is another focus at the institute. It is the study of inheritable traits that are not caused by changes in the underlying DNA sequence. Epigenetic mechanisms are crucial for the organization and utilization of our genetic information. Since the susceptibility to diseases can be promoted by epigenetic dysfunction, epigenetic research has far-reaching implications for diagnosis and therapy of human disease.

Facility Description

The MPI-IE Imaging Facility offers a large variety of microscopy techniques, image processing and analysis to MPI scientists only. Therefore, it currently manages 8 advanced fluorescence microscopes of various types, including five systems suitable for live samples, a biosafety level S2 containment, high-end workstations and advanced programs for bioimage analysis. The Facility staff assists about 80 users from MPI-IE in all microscopy-related subjects, including planning experiments, microscope selection, image acquisition and analysis. Usage of the Facility increased from total 2700 hrs in 2014 to 7165 hrs in 2016. To further improve the service and user experience, Facility staff continuously communicates with the research groups, informally and through regular Users Committee meetings. Staff members teach microscopy and image processing, from one-to-one hands-on sessions to various seminars and EMBO courses. Further, Imaging Facility is involved in method development. The Facility constantly renews its equipment and expands the arsenal of available techniques: in 2015, new inverted multi-photon system LSM 780 NLO was acquired; in October 2017, LSM 880 Airyscan Fast, the high-end confocal with recently invented Airyscan detector has been installed. Imaging Facility is a member of the German Society for Microscopy and Image Analysis and participates in the Microscopy and Image Analysis Platform Freiburg (MIAP).

Featured Instruments

• LSM 880 Airyscan Fast
High-end inverted confocal system equipped with recently invented Airyscan detector which enables one to significantly improve speed, sensitivity and/or resolution (up to 1.7 fold), in comparison to any conventional confocal system, while preserving versatility of the latter.

• Elyra PS1
A multi-modal system which combines PALM & dSTORM super-resolution, SIM super-resolution, total internal reflection (TIRF) and confocal imaging modes, which can be used for the same field of view.

• Cell Observer SD
A Nipkow spinning disc microscope, enables high-frame-rate and long-term observations of live samples with little photodamage, as well as fast acquisition of 3D datasets.

• LSM 780 NLO
An inverted combined multi-photon and confocal system enabling one to acquire high quality images deep in intact tissue.

• LSM 780
An inverted versatile confocal laser scanning microscope with spectral detectors, suitable for instance for simultaneous signal acquisition of multiple chromophores in any combinations, including live samples.

• Axiovert 200M
An epifluorescence microscope equipped with microinjection system and environment control unit.

Image Analysis Software

• Imaris
A “flagship” software package for multidimensional image visualization and quantitative analyses. We have multiple modules for surface rendering, object tracking, filament tracing, automated processing, integration of custom plug-ins from Fiji and Matlab; 3D co-localization.

• Huygens Essential
Leading dedicated software for image restoration based on deconvolution algorithms, which permits the recovery of objects from microscopic images inevitably degraded by blurring and noise.

• ImageJ / Fiji
The most popular open-source software for image analysis. “Wikipedia-style” software continuously developed by wide scientific community, with hundreds of specialized plug-ins and image analysis procedures. http://fiji.sc/Category:Tutorials

• Zen Blue / Zen Black (offline)
Softwares by Carl Zeiss for viewing and basic analyses of datasets acquired on Zeiss microscopes, without any export or conversion. Suitable namely for tile stitching, super-resolution SIM, single molecule localisation data processing. http://www.zeiss.com/microscopy/en_de/products/microscope-software/zen.html

• CellProfiler
Open-source software to quantitatively measure phenotypes from thousands of images automatically.  http://www.cellprofiler.org/