Pipette

Systems Biology Imaging

Andrew Woehler

About

Light microscopy imaging is at the heart of a wealth of research at the MDC and across the Biosciences. At the Systems Biology Imaging Platform in BIMSB, we provide access and support to both MDC-affiliated and visiting scientists in a range of state-of-the art microscopy and data analysis methods.

We offer consultations and collaborations to help create research workflows including custom building experimental parts, preparing samples, imaging & other light based techniques, and designing bespoke image analysis pipelines.

Overview

Our infrastructure incorporates a range of light-based biotechnology techniques, providing images across volume, time and spatial resolution scales. We have a well equipped lab space and workshop for preparing samples and experimental parts, a number of image and data processing tools, and can offer expertise to help with experimental design, light based measurements and image analysis solutions.

In addition to supporting the work of other researchers, we are also involved with a number of collaborations and projects of our own, and seek to foster interactions with industry partners to bring emerging imaging technologies to the campus.

Current Projects

We are working to adapt existing or developing novel technology including:

  • Small molecule and genetically encoded biosensors
  • Experimental multiplexing techniques
  • Advanced image analysis tools

to quantitatively study intracellular signal transduction and synaptic transmission. We aim at contributing to a better understand how information is processed at subcellular, cellular, and networks scales and how this processing is altered in neurological disorders.

 

Platform Video Tour

Beschreibung

The Systems Biology Imaging team members present a tour around the equipment and workspaces available in the platform.

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Example Image Gallery

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Events

Upcoming Events

Microscopy Club | monthly

 

Previous Events

11th Berlin Summer Meeting and BIMSB Opening Symposium | 25-27 October 2018

Leica workshop on Multiphoton Confocal and Advanced Live Cell Imaging | 19-22 September 2017

MDC Technology Training in Light Microscopy / Zeiss workshop | 11-13 July 2017

10th Berlin Summer Meeting "Imaging Gene Regulation from DNA to RNA to protein | 8-10 June 2017

EU-Life Course Biological Image Reconstruction and Analysis | 14-18 November 2016

Team

Group Leader

 

Dr. Andrew Woehler

101: Berlin Institute for Medical Systems Biology: 2.07

Andrew.Woehler@mdc-berlin.de

 

Technical Assistant

Agnieszka Klementowicz

101: Berlin Institute for Medical Systems Biology: 2.50.1

Agnieszka.Klementowicz@mdc-berlin.de

 

Scientists

Dr. Peran Hayes

101: Berlin Institute for Medical Systems Biology: 2.50.1

davidperan.hayes@mdc-berlin.de

 

Former Members

Dr. Nikita Vladimirov

101: Berlin Institute for Medical Systems Biology: 2.50.1

nikita.vladimirov@mdc-berlin.de

 

Dr. Anna Oliveras Martinez

anna.OliverasMartinez@mdc-berlin.de

 

Dr. Zohreh Farsi

Zohreh.Farsi@mdc-berlin.de

 

Dr. Marie Walde

Marie.Walde@mdc-berlin.de

 

Elisabeth Fritsch

 

Giulia Forcina

 

Linda Drewicke

 

Ecem Çakmak

Equipment

Confocal Microscopes

​​Leica SP8 Falcon (SMD)

Versatile confocal with a wide range of functionalities

Good for:

  • High resolution, 3D imaging of thicker samples.
  • Multi-channel imaging: customizable excitation & detection wavelengths to minimize crosstalk
  • Customizable image format & area eg for resolution optimization, FRAP, photoactivation...
  • Spectral scanning, FLIM & Fluorescence lifetime gating
  • User-friendly software

Specs:

  • White Light Laser coupled with an Acousto-Optic Beam Splitter to allow tunable illumination within a wavelength range of 470-670nm and a bandlet width of <3nm
  • 405nm near-UV diode laser
  • Leica DMi8 Microscope body
  • Prism detection system to facilitate tunable detection spectra control across an emission spectrum of 380-800nm
  • 4 Hybrid detectors & 1 PMT detector
  • Transmitted light detector
  • Chamber for CO2 and temperature control for live imaging
  • Options to control scan area, image format & aspect ratio and image rotation
  • λΛ-Scan Spectral scanning functions
  • Fluorescence Lifetime Imaging module and detection lifetime gating
  • Navigator module for large sample tile-scanning and automated multi-point imaging
  • Leica Lightning confocal deconvolution software

Leica SP8 STED

Confocal microscope with super-resolution capabilities

Good for:

  • High resolution, 3D imaging of thicker samples.
  • Super-resolution imaging (STED)
  • Multi-channel imaging: customizable excitation & detection wavelengths to minimize crosstalk
  • Customizable image format & area eg for resolution optimization, FRAP, photoactivation...
  • Spectral scanning, FLIM & Fluorescence lifetime gating
  • User-friendly software

Specs:

  • White Light Laser coupled with an Acousto-Optic Beam Splitter to allow tunable illumination within a wavelength range of 470-670nm and a bandlet width of <3nm
  • 405nm near-UV diode laser
  • 590nm STED laser
  • Prism detection system to facilitate tunable detection spectra control across an emission spectrum of 380-800nm
  • 2 Hybrid detectors & 2PMT detectors
  • Chamber for CO2 and temperature control for live imaging
  • Options to control scan area, image format & aspect ratio and image rotation
  • λΛ-Scan Spectral scanning functions
  • Detector lifetime gating
  • Lightning confocal deconvolution software

Andor Dragonfly 200 Spinning Disk

Spinning disk confocal for fast 3D imaging

 Good for:

  • High speed imaging to capture fast dynamic samples or image large volumes
  • Confocal optical sectioning to image thick samples in 3D at high resolution

Specs:

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Widefield Microscopes

Leica THUNDER Live Cell Imager

Fast, user-friendly and multi-functional widefield system

Good for: 

  • Fast imaging of large sample areas
  • A good option for thin samples
  • Multi-position acquisitions and stitched tile scans
  • Colour camera, eg for histology, H&E staining etc.
  • Multi-channel imaging with 8 LEDs
  • User-friendly software

Specs:

  • Leica LED8 Light Engine has 8 illumination LEDs with wavelength peaks at 395, 438, 475, 511, 555, 575, 635 and 730 nm
  • Compatible filter sets appropriate for most labels within the visible spectrum.
  • Leica DMi8 microscope body
  • Leica DFC 9000GT sCMOS monochrome fluorescence camera:
    • sensor size: 13.3mm x 13.3mm
    • number of pixels: 2048 x 2048
    • sensor pixel size: 6.5µm x 6.5µm
    • min exposure time: <12 ms
    • Bit depth: 12 bit / 16 bit
    • Max quantum efficitency: ~82% @ 580nm
  • Leica FLEXACAM C1 colour CMOS camera:
    • sensor size: 4.55 x 6.17mm (1/2.3")
    • number of pixels: 4000 x 3000 (12MP)
    • sensor pixel size: 1.55µm x 1.55µm
    • exposure time: 100µs - 120ms
    • colour depth: 3 x 8 bit
  • Navigator module for large sample tile-scanning and automated multi-point imaging
  • Leica Thunder widefield deconvolution software

To test/check possible microscope configurations, detection efficiency and potential crosstalk for your specific fluorophores, please follow this FPbase link.​​​​​

Nikon/Visitron iLas2 TIRF

Widefield system with TIRF, FRAP, FLIP and localised photoactivation capabilities

Good for:

  • TIRF microscopy, which can image a single thin slice (<100nm thick) at the sample-coverslip interface with high resolution & signal to noise ratio
  • FRAP & FLIP techniques to study molecular dynamics
  • Locally controlled illumination and photoactivation (eg for glutamate uncaging)
  • An alternative to the THUNDER for simple widefield imaging (brightfield, phase & polarisation contrast, DIC and epi-fluorescence)

Specs:

  • Four Coherent Obis laser illumination lines: 405, 488, 561 and 640nm
  • Visitron Systems Laser combiner
  • Gataca Systems iLas2 laser control platform for 360° spinning, uniform field TIRF with simultaneous FRAP, FLIP & photoactivation
  • Nikon Eclipse Ti microscope body
  • Visitron Systems VisiView Microscope control software
  • Photometrics Prime 95B back-illuminated sCMOS camera

 

Nikon / MMI LCM

Multi-channel widefield fluorescent imaging system with laser microdissection and single cell selection capabilities.

Good for:

  • Single Cell microdissection via laser ablation
  • Single cell micro-capillary aspiration & deposition
  • Multi-channel widefield imaging
  • Temperature & Co2 environmental control

Specs:

  • Lumencor SPECTRA III (L) Light Engine with 6 LED light sources with wavelength peaks at 390, 440, 475, 510, 555 & 575nm and 2 Lasers at 635 & 747nm
  • Prior OptiScan III motorised stage control system
  • Nikon Eclipse Ti 2 microscope body
  • Photometrics Prime 95B 22mm Camera
  • MMI CellEctor capillary cell sorting tool. Capable of manual and automated micro-capillary based single cell recognition, aspiration and deposition.
  • MMI CellCut laser microdissection tool. Designed for manual cell identification, cutting and extraction.
  • MMI CellTools software
  • OKOlab Temperature & CO2 environmental control setup.

 

Light-sheet Microscopes

Zeiss Z1

Dual light-sheet microscope for fast, gentle, 3D volume imaging

 

 

mesoSPIM

Open source, in-house built system for meso-scale volume imaging

 

Sample Preparation

Tissue clearing support

 

  • LifeCanvas EasyGel tissue-gel hybridisation system
  • LifeCanvas SmartClear II pro multi purpose clearing system
  • LifeCanvas Smart Label active immunostaining device  

 

Manufacturing

Mechanics

 

  • 3D Printer - FDM/FFF based: Ultimaker2 + Extended
  • 3D Printer - Resin based: FormLabs Form2
  • Milling/Drilling machine: Holzmann BF 16V
  • Bandsaw: Proxxon MBS 240/E
  • Jigsaw: Bosch PST 18 LI Cordless
  • Hot air gun: Einhell TH-HA 2000/1
  • Various hand tools, clamps etc

Electronics

 

  • Soldering station: Toolcraft ST-50 A
  • Oscilloscope: Rigol DS1054Z
  • Waveform generator
  • Multimeter

Optics

 

  • Spectrometer
  • Power meter
  • Refractometer
  • Various optics/optomechanics parts

Microfluidics

 

  • Soft lithography infrastucture
  • Microfluidics controllers

Publications

Training & Resources

The platform offers collaboration opportunities, consultation and training in project planning, sample preparation, image acquisition, data management and analysis. Please contact us for more details.

Training

Theoretical and hands on training required for all systems (est. 2 hrs).

Booking

Go to https://mdc.science-it.ch/ to register for our booking system. After registering, go to the browse tab, then resources, search for the instrument you are interested in using (i.e. SP8 SMD), click on the blue arrow under the device picture to request access. The platform will get an email and contact you to schedule a training session. After which we will grant you access and you can book the system anytime you like.

Resources

Refractive Index Matching

It is important to choose your imaging objective such that its refractive index matches as closely as possible that of your imaging mounting media

Refractive indices of objective immersion media
Water 1.33
Silicone 1.406
Glycerol 1.47
Oil 1.518

 

Refractive indices of standard mounting media
75% Glycerol   1.44
Vectashield   1.457
Mowiol   1.49
ProLong Gold

Fresh mounting

Cured for 1 day

Cured for 4 days

1.39

1.40

1.44

 

Useful Links

 

Dr. Andrew Woehler
Dr. Andrew Woehler