Platforms and facilities

SRCSB technology platforms

Cellular Analytics

The technology platform “Cellular Analytics” provides access to a wide spectrum of advanced light microscopy and cytometry equipment. The imaging technologies provided allow flexibility in addressing diverse scientific questions, in particular through gathering quantitative and real time information from biological systems that range from subcellular signal transduction networks to cell populations and tissues. Furthermore, a cell sorting unit allows multi-parameter analysis of cell suspensions and sterile cell sorting of up to four subpopulations in parallel. The platform is set up in dedicated laboratory and office spaces (Allmandring 5b, rooms 2.01 – 2.05) and operates as a multi-user facility open for all collaborators within the SRCSB.

The technology platform is scientifically coordinated through the Institute of Cell Biology and Immunology (Prof Dr Markus Morrison). Access to the facility and user support is coordinated through the platform manager Dr Stephan Eisler and his technical assistant Ms. Melanie Noack. The spectrum of activities includes, but is not limited to, providing training and support in routine microscopy and cell sorting applications, offering workshops in image analysis, establishment of advanced quantitative imaging and image analysis pipelines, and providing personalized support and consultation for independent research projects.


Fully automated epifluorescence microscope, located inside an incubator for longterm observation of living cells in up to six vessels simultaneously.

Real-time monitoring and analysis of multiple integrated live-cell assays.

Equipment: 4x/10x/20x phase contrast objectives, green and red fluorescence filters.

Applications (selection):
Apoptosis, Cytotoxicity, Proliferation, Spheroids, Scratch Wound Migration and invasion, chemotaxis, Dilution cloning, transfection efficiency, Cell-by-Cell Analysis 

Room: 2.04
Next generation confocal laser scanning microscope with super resolution and high speed modus. The 32 PMT Array detector of the Airyscan 2 increases the lateral resolution to 120 nm (lateral) and 350 nm (axial). The refined multiplex modus allows to optimize acquisition speed (up to 47 fps), bleaching/phototoxicity and resolution according to individual experimental demands in an intelligent manner.

The inverted microscope is equipped with 6 excitation lasers (405 nm, 445 nm, 488 nm, 514 nm 561 nm, 640 nm), incubation chamber, CO2 unit, Definite Focus 3 and AI Sample finder.
Additional software modules: FCS, FRET, Physiology, 3d-rendering

Plan-Apochromat 63x/1.4 Oil
LD LCI Plan-Apochromat 40x/1.2 Multi-Immersion
C-Apochromat 40x/1.2 W
Plan-Apochromat 20x/0.8
EC Plan-Neoflura 10x/0.3

Confocal imaging with super resolution. Gentle live cell imaging with high speed and sensitivity. FCS, FRET, FRAP, photoactivation, Colocalization

The LSM710

Room 2.04
Inverted confocal laser scanning microscope equipped with 4 Lasers providing excitation wavelengths of 405 nm, 458 nm, 488 nm, 514 nm, 561 nm and 633 nm.

Three detectors including a spectral detector for Lambda-mode, T-PMT for DIC images and a large incubation unit.

Objectives: EC Plan-Neofluar10x/0.3, Plan-Apochromat 20x/0.8, EC Plan-Neofluar40x/1.3 DIC,
Plan-Apochromat 63x/1.4 Oil DIC

Applications: 3d z-stacks in high resolution, live cell imaging, FRET, FRAP, Photoactivation, colocalization, linear unmixing

Zeiss Cell Observer Z1
The Zeiss Cell Observer Z1

Room 2.01
Inverted epifluorescence microscope equipped with ApoTome, Definite Focus 1, Colibri LED light source and a large incubation unit.
CCD camera: Axiocam MRm

Objectives: EC Plan-Neofluar10x/0.3, Plan-Apochromat 20x/0.8, LD Plan-Neofluar 40x/0.6 Korr Ph2, Plan-Apochromat 63x/1.4 Oil DIC

Applications: Long-term live cell imaging, multipositioning, 3d z-stacks with Apotome

Room 2.01
Inverted confocal Spinning-Disk Microscope equipped with Yokogawa CSU-X1 Spinning Disk Unit, Laser-TIRF3, Definite Focus 2, a large incubation unit and UGA-42-Firefly point scanning device (Rapp Optoelectronics) for photomanipulation experiments.

6 acquisition lasers: 405 nm, 445 nm, 488 nm, 514 nm, 561 nm, 638 nm
2 photomanipulation lasers: 473 nm, 515 nm

CCD cameras Axiocam 503 mono (2x)
EMCCD camera: Photometrix Evolve 512

Objectives: Plan-Apochromat 10x/0.45, Plan-Apochromat 20x/0.8, LD LCI Plan-Apochromat 25x/0.8 Imm Korr DIC, Plan-Apochromat 40x/1.4 Oil DIC, Plan-Apochromat 63x/1.4 Oil DIC, alpha Plan-Apochromat 100x/1.46 Oil DIC

Applications: Fast confocal long term live cell imaging, multipositioning, fast 3d z-stacks, TIRF microscopy, simultaneous acquisition of two fluorescent channels in dual camera mode, FRET, FRAP, photoactivation, Colocalization

Nikon Ti-E TIRF
Nikon Ti-E TIRF

Room 2.01
Inverted TIRF microscope equipped with three lasers (488 nm, 561 nm, 640 nm) and EMCCD camera (Andor iXon Ultra  897)
Objectives: CFI Apochromat 10x/0.25, CFI Apochromat TIRF 100x Oil/1.49

Applications: Fast confocal live cell imaging, fast 3d z-stacks, TIRF microscopy, FRET, FRAP, Photoactivation, Colocalization

Applications: TIRF Microscopy, single molecule tracking

Idea Biomedical Hermes WiSCAN
Idea Biomedical Hermes WiSCAN

Room 2.04
High content screening microscope for the automated acquisition of images in up-to 1536-well plates in five channels (TL, blue, green, red, far red) equipped with live-cell package.

Objectives: 10x, 20x, 40x
Analysis software suite: WiSoft Minerva

Applications: High content screening, phenotypic screening, Live cell imaging

Fully automatized zoom microscope equipped with fluorescence in three channels (blue, green, red), 16x zoom optics and an adjustable field of view.

Objective: Plan Apo Z 0.5x/0.125
Camera: AxioCam 512 Color

Applications: Imaging of large samples/fields of view, preparative microscopy



Room 2.05
BD FACS Aria III, equipped with 4 Lasers (405 nm, 488 nm, 561 nm, 633 nm), 16 fluorescent detectors, FSC, SSC, a cooling unit and multiwell plate sorting option.

The system allows sorting of up to four populations simultaneously.  

Leica SPL
The Leica-SPL

Room 2.01
Inverted epifluorescence microscope equipped with Sutter DG-4 excitation light source and Improvision orbit emission filter wheel for fast image acquisition.
The microscope has also a eppendorf FemtoJet microinjection station and a large incubation unit available.

Objectives: 10x, 20x, 25x, 40x, 63x,

Applications: Live cell imaging, FRET, microinjection

Location: Technology Platform Cellular Analytics

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Systems Transcriptomics Platform

The technology platform “Systems Transcriptomics” provides access to state-of-the art methods in the analysis of gene regulation. The current activities are centered around three pilars,

  • Imaging-based analysis of gene expression heterogeneity at the single-cell level by single-molecule FISH and reporter gene assays
  • Genome-wide analysis of global gene expression programs by single-cell and bulk RNA sequencing
  • Bioinfomatic analysis, machine learning and quantitative kinetic modeling of quantitative gene expression data

The platform is scientifically coordinated by the Institute for Industrial Genetics (Prof. Stefan Legewie, Departement of Systems Biology), and involves close interactions with other SRCSB groups and the Cellular Analytics platform.

The spectrum of activities includes training and support in routine methods and analysis pipelines in the context of the three pilars. User support and consultation for independent research projects is provided by Raymond Gosliga and Stefan Legewie. Further activities include the organization of joint seminars/workshops, the establishment of joint teaching modules and the coordination of joint funding applications. To further develop this platform and the expertise on quantitative gene expression analysis, user committees consisting of local experts are assembled for each of the three platform pillars.


This image shows Stephan Eisler

Stephan Eisler


Scientific staff

This image shows Melanie Noack

Melanie Noack


Technical staff

Stefan Legewie

Prof. Dr.

Member of the SRCSB Board of Directors

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