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Our Microscopy Services and Instruments

The Zeiss 880 upright laser scanning confocal microscope can be used for multicolour fluorescence imaging as well as for live-cell imaging. The system is equipped with 2 conventional photomultiplier tubes and a high sensitive GaAsP detector as well as an airyscan detector for higher resolution confocal scanning (resolution in x,y,z increased by a factor of max. 1.7) and a FAST-Scan Modul.


  • Zeiss Axio Examiner.Z1


  • HXP 120V (visual observation)
  • LSM880 laser modules:
    • Diode laser 405 nm
    • Argon Multiline laser 458 / 488 / 514 nm
    • Laser 561 nm
    • HeNe laser 594 / 633 nm


  • 10x/0.45NA Plan-Apochromat (a=2.0 mm)
  • 20x/0.8NA Plan-Apochromat (a=0.55 mm)
  • 20x/1.0NA W Plan-Apochromat DIC (a=1.7 mm)
  • 63x/1.4NA Oil Plan-Apochromat DIC (UV)VIS-IR (a=0.13 mm)
  • 63x/1.2NA W Korr C-Apochromat (a=0.28 mm)


  • 2 Photomultiplier tubes
  • 1 GaAsP Detector
  • 1 Airyscan detector


  • ZEN Black 2.3

Fluorescence filter sets:

For visual observation filtersets for DAPI, GFP, Cy 3 and Cy 5 are available.

(Filter set number)
ExcitationBeam splitterEmission
DAPI (Zeiss FS49)G365FT 395BP 445/50
GFP (Zeiss FS38)BP 470/40FT 495BP 525/50
Cy 3 (Zeiss FS43)BP 545/25FT 570BP 605/70
Cy 5 (Zeiss FS50)BP 640/30FT 660BP 690/50

The Zeiss AxioImager.Z1 light microscope offers acquisition of conventional fluorescence images as well as optical sectioning with an Apotome system.


  • Zeiss AxioImager.Z1


  • X-CITE 120 Mercury short arc lamp
  • XBO 75 Xenon short arc lamp


  • 2.5x/0.075 Plan-Neofluar
  • 10x/0.3 Plan-Neofluar
  • 20x/0.5 Plan-Neofluar
  • 40x/1.2 W C-Apochromat
  • 63x/1.2 W C-Apochromat


  • Zeiss AxioCam MRm



  • Zeiss AxioVision 4.8

Fluorescence filter sets:

(Filter set number)
ExcitationBeam splitterEmission
DAPI (Zeiss FS49)G 365FT 395BP 445/50
CFP (Zeiss FS47 HE)BP 436/25FT 455BP 480/40
GFP (Zeiss FS38 HE)BP 470/40FT 495BP 525/50
DsRed (Zeiss FS43 HE)BP 550/25FT 570BP 605/70
mPlum (Zeiss FS64 HE)BP 587/25FT 605BP 647/70
Cy 5 (Zeiss FS50)BP 640/30FT 660BP 690/50
Cy 5.5 (AHF F46-022)BP 655/40FT 685BP 716/40
Cy 7 (AHF F36-577)BP 708/75FT 757BP 809/81


This 3D light-sheet fluorescence microscopes (LSFM) also called Single/Selective Plane Imaging Microscopes (SPIM) provide high speed optical sectioning in low and high optical resolution of larger tissue samples (e.g. tissue slices) as well as organoids, cells and small model organisms (e.g. drosophila larvae, zebra fish). The system can be used for long-term live cell imaging due to an incubation system (heating, cooling, CO2 chamber) as well as for deep tissue imaging of cleared samples. The system provides a broad range of excitation wavelengths and multiview imaging.


  • Zeiss Lightsheet.Z1


  • Dual side illumination
  • Pivot scanner technology alters the angle of the light sheet upwards and downwards during scanning to avoid shadow artifacts
  • Available laser lines: 405 nm, 445 nm, 488 nm, 515 nm, 561 nm, 638 nm
  • Illumination optics: 5x/0.1 and 10x/0.2


  • 5x/0.16 EC Plan-NEOFLUAR
  • 20x/1.0 Clr Plan-Apochromat Korr nd=1.38
  • 20x/1.0 Clr Plan-Neofluar Korr nd=1.45
  • 20x/1.0 W Plan-APO DIC
  • 63x/1.0 W Plan-APO VIS-IR


  • pco.edge sCMOS camera, 30 fps at 960 x 1024, pixel size 6.5 µm


  • Zeiss ZEN system 2014 for lightsheet Z.1
  • Arivis Vision 4D

Fluorescence filter sets:

  • Filtersets for various standard fluorophores are available: DAPI, GFP, mCherry, CFP, YFP, Cy3, DRAQ5

This 3D lightsheet fluorescence microscope (LSFM) - also called Single / Selective Plane Imaging Microscopes (SPIM) - provides high speed optical sectioning of large cleared samples, such as whole mouse brains, at a lower magnification.

This system is equipped with a white light laser which provides a broad range of excitation wavelengths, potentially allowing us to excite fluorophores with excitation wavelengths even in infrared. This microscope is optimized for the imaging of large cleared samples. The system can also be used for in vivo imaging at room temperature.


  • LaVision UltraMicroscope II, Zoom box configuration


  • Dual side illumination with triple sheet optics on each side generating laser light sheet perpendicular to the direction of detection (Minimum thickness: <4.5 μm @ 488 nm for one individual sheet).
  • SuperK EXTREME EXW12 White light laser system with a wavelength range from 465 to 2400 nm.

Fluorescence filter sets:

CFP, GFP470/30535/30
Cy 3520/40585/40
Cy 5640/30690/50
Cy 7710/75810/90


Microscope: Olympus MVX 10 Zoom Body. The variable zoom body provides magnification steps from 0.63x to 6.3x.


  1. Olympus MVPLAPO 2x/NA 0.5 Dry lens,
    equipped with a dipping cap including correction optic, working distance > 5.7 mm.
  2. LaVision BioTec PLAN 12x/NA 0.53 xDISCO, working distance 9.0 mm.
    Two dipping lenses optimized for liquids with refractive index of 1.56 ± 0.1, or 1.45 ± 0.1 respectively.


  • Andor Zyla 4.2 Plus sCMOS camera


  • LaVision BioTec ImSpector Software

The Axio Scan 7 is a powerful slidescanner for high throughput automated image acquisition of brightfield as well as multi-channel fluorescence slides up to NIR.

Additionally it's equipped with a phase and relief contrast module (TIE - Transfer of Intensity Equation) which helps to detect transparent tissue or protect samples with sensitive fluorescent dyes from bleaching.

Axio Scan 7 features high numerical aperture dry objectives for high resolution and is able to scan whole 3D volumes.


  • automated upright slide scanning microscope
  • slide holders for standard slides (26 x 76mm) or big slides (52 x 76mm)


  • transmitted light LED (Colibri 7: 385 nm / 430 nm / 475 nm / 555 nm / 590 nm / 630 nm / 735 nm)


  • 5x/0.25NA Plan-Fluar (a=12.5 mm) M27
  • 10x/0.45NA Plan-Apochromat (a=2.1 mm) M27
  • 20x/0.5NA EC Plan-Neofluar M27 (a=2 mm) (not suitable for fluorescence)
  • 20x/0.8NA Plan-Apochromat (a=0.55 mm) M27
  • 40x/0.95NA Plan-Apochromat (a=0.25 mm) M27

Fluorescence filter sets:

DyeExcitationBeam splitterEmission
DAPI385FT 405BP 425/30
AF430430FT 450BP 467/24
AF488, Cy 2, OPAL520475FT 493BP 524/50
AF546, AF555, Cy 3, OPAL570*555FT 573BP 595/31
AF594*590FT 611BP 634/38
AF633, AF647, Cy 5, OPAL690630FT 653BP 709/100
AF740, AF750, Cy 7735FT 762BP 785/38

*Can be used only alternatively, not in combination


  • AxioCam 712 mono, 14 bit, pixel size 3.45 µm, 4096 x 3008 Pixel
  • AxioCam 705 color, 14 bit color camera, pixel size 3.45 µm, 2464 x 2056 pixel


  • ZEN Blue 3.5

Sample Submission Form for Slide Scanner

The Celldiscoverer 7 is highly automated boxed inverted LSM900 with Airyscan 2,dedicated tohigh contentscreening projects a well as imaging under consistent conditions.  You can use a widefield or confocal mode. The guided acquisition module enables fully automated imaging setups with initial large widefield overviews, image analysis to identify obcects of interest in the overviews and subsequent high-resolution imaging, z-stacks of those identified positions.


  • automated inverted confocal microscope (LSM900 with Airyscan 2)
  • widefield with LED fluorescence and transmitted light
  • slide holders for slides, dishes and plates
  • incubation / fully integrated climate control
  • automated stage and focus

Light sources:

  • Colibri 7 LED (385nm/420nm/470nm/520/567nm/590nm/625nm)
  • LSM900 Diodenlaser (405nm, 488nm, 561nm, 640nm)


  • 5x/0.35 Plan-Apochromat (WD 3.99 mm)
  • 20x/0.7 autocorr Plan-Apochromat (WD 1.33 mm)
  • 20x/0.95 autocorr Plan-Apochromat (WD 0.4 mm)
  • 50x/1.2W autocorr Plan-Apochromat (WD 0.4mm)

Afocal magnification changer (0.5x / 1.0x / 2.0x) is available for all objectives

The 50x is equipped with automated water dispenser.

Camera System:

  • AxioCam 512 mono,  64 bit, pixel size 3.1 µm, 4250 x 239 pixel


  • ZEN Blue 3.7

Fluorescence filters:





Set 90

BP 385/30
+ BP 469/38
+ BP 555/30
+ BP 631/33

QBS 405
+ 493
+ 575
+ 631

QBP 425/30
+ 514/30
+ 592/25
+ 709/100

Set 91

BP 423/44
+ BP 511/44
 + BP 591/27

TBS 450
+ 538
+ 610

TBP 467/24
+ 555/25
   + 687/145

Set 92

BP 385/30
+ BP 469/38
+ BP 591/27

TBS 405
+ 493
+ 610

TBP 425/30
+ 524/50
   + 688/145


  • Visiopharm, AI based software tool for standardized, quantitative image analysis of histological section
  • ZEN Blue for Image Postprocessing and Analysis
  • Visison 4D (ARIVIS) for xD visualization and quantitative structural analysis of tissue morphology

CF-PTA provides access to and training on high-end light microscopy equipment and to selected image processing software, as well as advice on special sample preparation.
To obtain access to any microscope please contact us.

1.    Initial project meeting at an early stage

For new imaging projects, an initial meeting is mandatory to determine the optimally suited approach concerning sample preparation by the user and microscopic hardware to be used.

2.    Project proposal

Furthermore, the submission of a project proposal is required. Please include any information needed to provide a clear and solid understanding of your goals and expectations for your project. Please fill in the project proposal template and mail us.

3.    Training

For all instruments, there is an initial practical training given by a staff member of the core facility.

Our Contact

Core Facility Pathology and Tissue Analytics

Ingolstädter Landstraße 1 85764 Neuherberg, Building 37, Room 003