Here you can find which equipment the Core Facilities use or offer for their services, sorted by units.
High-speed 4-way cell sorter (18 fluorescence parameters)
Lasers and filters:
- 355nm (UV): 450/50, 740/35
- 488nm (blue): 530/30, 695/40
- 405nm (violet): 450/50, 525/50, 610/20, 660/20, 710/50, 780/60
- 561nm (yellow-green): 586/15, 610/20, 670/14, 710/50, 780/60
- 633nm (red): 670/30, 730/45, 780/60
High-speed 4-way cell sorter (18 fluorescence parameters)
Lasers and filters:
- 355nm (UV): 450/50, 740/35
- 405nm (violet): 450/40, 525/50, 610/20, 660/20, 710/50, 780/60
- 488nm (blue): 530/30, 695/40
- 561nm (yellow-green): 582/15, 610/20, 670/14, 710/50, 780/60
- 633nm (red): 670/30, 730/45, 780/60
High-end analysis (64 fluorescence parameters)
Lasers:
- 355nm (UV): 16 Kanäle
- 405nm (violet): 16 Kanäle
- 488nm (blue): 14 Kanäle
- 561nm (yellow-green): 10 Kanäle
- 640nm (red): 8 Kanäle
High-end analysis (38 fluorescence parameters + 3 Scatter Channel)
Lasers:
- 405nm (violet): 16 channels
- 488nm (blue): 14 channels
- 640nm (red): 8 channels
High-end analysis (19 fluorescence parameters)
Lasers and filters:
- 355nm (NUV): 450/45, 525/40, 675/30
- 405nm (violet): 450/45, 525/40, 610/20, 660/20, 780/60
- 488nm (blue): 525/40, 610/20, 690/50
- 561nm (yellow-green): 585/42, 610/20, 675/30, 690/50, 780/60
- 638nm (red): 660/20, 712/25, 780/60
Our instruments are shared between the Units Flow Cytometry, Proteomics and Imaging. (See „Instruments Mass Cytometry“)
High-end flow imaging cell analyser (12 imaging channels)
Magnification: 20x, 40x, 60x
Lasers and filters:
- 405nm (violett): 457/45, 537/85
- 488nm (blau): 528/65, 577/35, 610/30, 702/85, 762/35
- 561nm (gelb-grün): 577/35, 610/30, 702/85, 762/35
- 642nm (rot): 702/85, 745/35
Immuno-capture chip-based system for analyzing the smallest extracellular vesicles (Tetraspanines: CD9, CD63, CD81)
High-end analysis (18 fluorescence parameters)
Lasers and filters:
- 355nm (UV): 450/50, 570/30
- 407nm (violet): 450/50, 525/50, 610/20, 660/20, 710/50, 780/60
- 488nm (blue): 530/30, 695/40
- 561nm (yellow-green): 586/15, 610/20, 670/30, 696/40, 780/60
- 633nm (red): 670/30, 730/45, 780/60
fully closed and sterile cartridge based system, one-way sorter
- 405nm (violet): 2 channels
- 488nm (blue): 4 channels
- 640nm (red): 2 channels
Analysis of small particles
Laser:
- 488nm for detection of one fluorescent dye
The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification, and quality control of DNA and RNA.
The CFX96 Touch System is a real-time PCR detection system equipped with a 6-color detection system in 96-well format.
Up to 1500 GB output with 25 million sequencing reads and 2 × 75 bp read lengths.
Up to 15 GB output with 25 million sequencing reads and 2 × 300 bp read lengths.
Up to 120 GB output with 400 million sequencing reads and 2 × 150 bp read lengths.
Up to 360 GB output with 1200 million sequencing reads and 2 × 150 bp read lengths.
Single cell analyzes based on the so-called “Next GEM technology”.
The NanoDrop ® ND-1000 is a full spectrum spectrophotometer (220-750nm) that measures 1ul samples with high accuracy.
Long-read single-molecule sequencing technology using nanopores
- Maximum throughput: 10-20 GB (MinIon); 50-100GB (GridIon)
- Read length: 20 B to > 2 MB
- Maximum number of “flow cells”: 1 (MinIon); 5 (GridIon)
Qubit assays provide accurate, specific and sensitive quantification of DNA and RNA using fluorescence measurements.
An instrument to facilitate the transfer of transcriptomic probes from sectioned tissues to Visium Slides.
The two “Axio Imager M2” from Zeiss are upright wide-field microscopes with the option of transmitted light and fluorescence images.
They are equipped with a 5 megapixel CCD camera (MRc5 Axiocam) and integrated into the current “Zen blue” software platform.
The system enables the following applications:
- Transmitted light photographs (in color)
- Multifluorescence images (filters: DAPI, GFP, Cy3, Cy5)
- Polarization images (e.g. for Picro-Sirius-Red staining)
The Axioscope is a simple upright microscope with the ability for transmitted light and darkfield applications. It is used to view tissue sections and is not equipped with a camera.
The “Axiovert” from Zeiss is an inverted cell culture microscope with the option for transmitted light and fluorescence images. The microscope is equipped with a 5 MP CCD camera and connected to a workstation (Zen software).
The system enables the following applications (or combinations thereof):
- Cell culture images with phase contrast
- Time series
- Fluorescence with GFP or rhodamine filter
The Live Cell Imaging Microscope IX83 is an inverted wide-field microscope from Olympus. It is equipped with a high-end camera (Hamamatsu Orca Flash 4 sCMOS), a color camera (UC90-Olympus), a large incubation chamber for constant temperature and additional small incubation chambers (Ibidi) for supplying CO2 and air humidification.
The TIRF option is based on a motorized integrated TIRF illumination combiner with 4 laser fiber inputs and one input for wide field illumination.
The system enables the following applications or combinations thereof:
- Phase contrast or DIC images
- Fluorescence images (filters: DAPI, GFP, Cy3, Cy5, CFP, YFP)
- Z-Stack (3D)
- Time series
- Shooting from different positions
- Large overview images
- Live cell microscopy
- TIRF recordings (laser: 405nm, 488nm, 561nm)
- Cryostat
The Leica CM3050S cryostat can be used to produce frozen sections of various thicknesses. The device is motorized and therefore enables precise cutting and the production of thin series cuts. - Microtomes
The two Leica RM2255 rotary microtomes can be used to produce paraffin sections of various thicknesses.
The SP8 from Leica is an inverted point laser scanning microscope. It is equipped with a tuneable white light laser and 2 PMT detectors, 2 HyDs (GaAsP detector for gated imaging) and 1 HyD S (for photon counting and FLIM)
The system enables the following applications (or combinations thereof):
- Confocal fluorescence recording (laser: 405nm + pulsed white light laser 470–670nm)
- Z-Stack (3D)
- Time series
- Acquisition of various positions
- FRET analyses
- Online intensity measurements
- FLIM (fluorescence lifetime microscopy)
- Lightning mode (adaptive deconvolution for higher resolution)
- Light Sheet (for fast 3D imaging of cleared / transparent samples)
The LSM 900 from Zeiss is an inverted point laser scanning microscope. It is equipped with 4 solid-state lasers and 3 sensitive GaAsP detectors. The system is characterized by great user-friendliness (software: Zen blue).
The system enables the following applications (or combinations thereof):
- High-resolution multifluorescence images (laser: 405nm, 488nm, 555nm, 639nm)
- Z-Stack (3D)
The LSM 980 is an inverted point laser scanning microscope. It is equipped with a highly sensitive 32 GaAsP (Gallium Arsenide Phosphide), 2 PMTs and 1 AiryScan2 detector for super-resolution or high-speed recordings. An incubation chamber also enables optimal conditions for living cells. Software: Zen blue 3.3
- High-resolution confocal fluorescence images (laser: 405nm, 445nm, 488nm, 514nm, 561nm, 594nm, 639nm)
- Z-Stack (3D)
- Time series, live cell imaging
- Multiple positions
- Tiles, large overview images (with sample navigator)
- FRET, FRAP
- Online intensity measurements
- “Super-resolution” images with the Airyscan 2
The MACSima imaging platform is a fully automated fluorescence microscope that enables 200+ proteins to be imaged on a single sample (FFPE, fresh frozen or cell culture), providing access to spatial proteomics.
- Fully automated cyclic staining, capture and destaining.
- Free choice of antibodies
- <400 nm optical resolution
- MACS® iQ analysis software
- Multiomics through additional recording of up to 27 RNAs
The Spinning Disk Microscope from Olympus enables confocal imaging with a lateral resolution of up to 150 nm, up to 50x faster than classical laser scanning microscopes.
The system enables the following applications (or combinations thereof):
- Fast and mild confocal fluorescence imaging (lasers: 405, 488, 561, 640 nm)
- Parallel multi-channel imaging using 2 ORCA-FUSION cameras (Hamamatsu)
- High resolution (150 nm) through additional SoRa spinning disk
- Live-cell microscopy
- Z-stack, time series and multi-position
- Objectives: 4x dry, 10x dry, 20x dry, 30x silicone oil (NA 1.05), 60x silicone oil (NA 1.3), 100x silicone oil (NA 1.35)
- cellSens Dimensions software (incl. deconvolution)
The ONI Nanoimager is a dSTORM microscope that achieves a resolution of 20 nm, 10x better than a standard confocal microscope.
- High-resolution multi-colour fluorescence images (laser: 405nm, 488nm, 561nm, 640 nm)
- 20 nm optical resolution using Stochastic Optical Reconstruction Microscopy
- Special modules for analysing extracellular vehicles (EVs).
- Online analysis software CODI
The Lumar is a motorized stereo microscope from Zeiss with the option for transmitted light and fluorescence images. The microscope is equipped with a 5 MP CCD camera and connected to a workstation (Zen blue).
The system enables the following applications (or combinations thereof):
- Ideal for preparing larger samples
- Transmitted light images
- Multifluorescence images (filter: DAPI, GFP, Rhodamine, Cy5)
- 3D
- Time series
The TissueFAXs is an automated slide or plate scanner based on an Axio Observer from Zeiss. 12 slides or 2 plates can be loaded onto this device. It is equipped with a color camera (Baumer HXG40c) and a fluorescence camera (Hamamatsu Orca Flash 4.0) for recording up to 5 fluorescence channels (filter sets: DAPI, GFP, Cy3, Cy5, C7).
The HistoQuest and TissueQuest analysis software is available on one of the workstations in the facility.
The system enables the following applications (or combinations thereof):
- Automated multi-channel recordings
- Individually definable region of interest (ROI)
- Automated single cell detection with patented algorithms
- Forward gating from the individual cell to the scattergram
- Backward gating from the individual point in the scattergram to an individual cell in the sample
- Accurate analysis of cells by gating specific regions on a dot plot
The PhenoImager slide scanner can record bright-field and fluorescence images. Up to 80 slides can be scanned in one go.
7 to 9 colors can be scanned multispectrally, which are then spectrally separated. Scanning TMA slides is also possible.
Filter sets:
- DAPI, Opal 570, Opal 690
- Opal 480, Opal 620, Opal 780
- Opal 520
Translated to other dyes:
- Opal 480 similar to Coumarin
- Opal 520 similar to Alexa488, FITC, Cy2, GFP
- Opal 570 similar to Alexa555, Cy3
- Opal 620 similar to Alexa594, Texas Red, RFP
- Opal 690 similar to Alexa660-700, Cy5
- Opal 780 similar to Alexa750, Cy7
Various commercial analysis software packages are available to users. For all images taken in the Imaging Facility, the analysis software can be used free of charge on the workstations.
- Arivis 3D, 4D Browser:
For visualization of Z-stacks in 3D, 4D. The following analyzes are also possible: FRET, colocalization, ratio measurements, 4D movies with storyboard, native resolution screenshots, simple dynamics, extended focus module, record macros and scripting (Python)
- HALO analysis software:
Easy-to-use analysis software for brightfield and fluorescence images. Available modules: Highplex Fluorescence, Multiplex IHC, Immuncells, Deconvolution, Area Quantification, Muscle Fibers, Object co-localization as well as HALO AI
ICP-TOF-MS technology. Suitable for multiplexed antibody-mediated analysis of single cells (single cell proteomics)
CyTOF technology coupled with laser ablation of tissue/ cell material on glass slides. Suitable for studying tissue architecture and in-depth phenotyping of cells on subcellular resolution
We offer our customers access to the following analysis programs:
- Maxpar Pathsetter (Standard Biotools)
- FCS Express (De Novo Software)
- Cytobank (Beckman Coulter)
- FlowJo (BD Biosciences)
To reduce sample complexity, the Proteomics Unit provides the following separation systems:
- Ultimate 3000 (Thermo Fisher) HPLC fractionation system for variable flow rate separation and fraction collection.
- Gel-based methods - 1D or 2D fractionation of intact proteins (incl. isoforms and post-translational modifications)
The Proteomics Unit operates the following LC-MS systems:
- Orbitrap Exploris 480 MS with FAIMS (Thermo Fisher) with Ultimate 3000 (Thermo Fisher) nano-HPLC separation system.
- Orbitrap QExactive Plus (Thermo Fisher) with Ultimate 3000 (Thermo Fisher) nano-HPLC separation system
- TIMS-ToF Pro (Bruker) with Ultimate 3000 (Thermo Fisher) nano-HPLC separation system
- maXis II qToF (Bruker) with Ultimate 3000 (Thermo Fisher) nano-HPLC separation system
- QTrap 6500 (SCIEX) with LC20 AD XR (Shimadzu) micro-HPLC separation system
For spatially resolved analysis of proteins or for targeted analysis of proteins at the single cell level, the Proteomics Unit operates the following technologies:
- Rapiflex MALDI Tissuetyper (Bruker)
- HTX-M5 Sprayer (HTX Imaging)
- Helios CyToF ICP-MS for Flow-ICP-MS and Laser Ablation-ICP-MS Imaging (together with the Core Facilities Flow Cytometry and Imaging)