Technologies & Services

Technologies & Services

Imaging Facility

MPI-IE users should consult our intranet webpage for more information on the technologies, instruments, assistance and access modalities!

  • Color bright field microscopy (“immunohistochemistry imaging”)
  • Epifluorescence
  • Laser scanning confocal microscopy
  • Nipkow Spinning disk
  • Multi-photon
  • Light sheet fluorescence microscopy
  • Total internal reflection microscopy (TIRF)
  • Optical tissue clearing (sample preparation)

Super resolution techniques:

  • 3D Structured Illumination (SR 3D SIM)
  • Single molecule localization microscopy (PALM, STORM, GSD etc)

All imaging modes (except color bright field and Apotome optical sectioning) can be applied to living samples, thanks to built-in and mobile incubation units for CO2 and temperature control. Imaging of Biosafety level 2 samples is possible in confocal and multi-photon modes at Imaging Facility’s S2 room

Instruments & image analysis tools

LSM880 Airyscan FAST and LSM900 Airyscan2

… high-end confocal systems equipped with “Airyscan” array detectors which enable one to significantly improve speed, sensitivity and/or resolution (up to 1.7 fold), in comparison to any conventional laser scanning confocal.

Elyra PS1

…an inverted multi-modal system which has PALM&dSTORM super-resolution, SIM super-resolution, total internal reflection fluorescence (TIRF) and confocal (LSM) imaging modes. This permits, for instance, to acquire images of the same areas of interest both at sub-diffraction resolution (<100 nm (“super-resolution”) and in LSM mode which permits flexibility of detection settings and large fields of view. (Instrument of Akhtar Department)

Cell Observer Spinning Disc

… an inverted Nipkow spinning disc confocal microscope, enables high frame rate and/or long-term observations of live samples with little photodamage, as well as fast acquisition of 3D datasets with efficient optical sectioning.


… inverted laser scanning confocal microscope, a versatile, ”work horse” system possessing multiple laser lines spanning the whole visible light spectrum, and “tunable” spectral detectors, thus distinguishing signals from multiple fluorophores with overlapping spectra. This gives the users the full flexibility in the choice and combinations of multiple fluorescent labels in the same sample. Control of illumination power in each pixel of the field of view makes this microscope ideally suited for photoperturbation techniques (such as FRAP, FLIP, photoactivation, etc.) which provide information about the dynamics of molecules and subcellular components in living cells.


…inverted combined multi-photon and confocal system which can acquire high quality images >100 micron deep in intact tissue samples. In addition, all functionalities of LSM780 confocal are possible.

Lightsheet Z1

… a light sheet fluorescence microscope with built-in incubation chamber. Its light path configuration (illumination perpendicular to detection), dual-side illumination and sample rotation permit fast 3D image acquisition of very thick (mm-scale) samples with extremely low photodamage. The instrument is suitable for (living) samples in water and optically cleared tissues in refractive index-matching media with RI from 1.38 to 1.45 (Instrument of Akhtar Department).

AxioImager Apotome and Apotome2

… upright microscopes suitable for fixed samples only. These user-friendly instruments can deliver 3D images with high resolution in z-dimension when structured illumination (SIM) via the Apotome module is applied (optical sectioning without pinholes). Color brightfield mode permits analysis of classically stained histology sections (immunohistochemistry, IHC).


… an inverted microscope for epifluorescence and transmitted light imaging. Environment control box (temperature, humidity, CO2) is built “around” the microscope stand, and thus permits access to the sample during image acquisition. The instrument is most suitable for time-lapse series when high resolution in z is not needed (e.g. cell migration).


A versatile commercial software package for visualization and analysis of multidimensional images, including very large datasets (>10 GB). Multiple modules permit various tasks, such as manual and automatic segmentation (also machine learning-based), object tracking, surface rendering, particle analysis, 3D tile stitching.


Advanced commercial software for image restoration based on deconvolution algorithms which permits users to recover image information of objects from various types of fluorescence images affected by out-of-focus light blurring and electronic noise. The software includes other image analysis tools (tiles stitching, multiple view fusion, aberration corrections etc).


The most popular and versatile open-source scientific image processing software, for which dozens of plugins were created by scientific community to address a great variety of image analysis tasks.

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