DBM Microscopy Core Facility

Light microscopy has revolutionized modern biology by creating a window for researchers to “see” the cellular and molecular world. The DBM Microscopy Facility enables researchers with limited microscopy knowledge to become experts and it allows experts to do creative experiments.

The DBM currently holds two microscopy facilities located at Hebelstrasse and at Mattenstrasse. Both facilities are used free of charge and there are more than 20 microscopes of various types available.

All the academic microscopy facilities in Basel form an interactive network called the Microscopy Network Basel (MNB), composed of the DBM, Biozentrum, D-BSSE, and FMI facilities. This facilitates exchange, fosters collaborations, and provides a wide net of
microscopy possibilities across the Basel academic landscape.

Our outlook is to continue raising the basic level of microscopy at the DBM while also extending the frontiers of what is possible in super-resolution microscopy. We are developing microscopy courses in house and in the Basel area in collaboration with the MNB, and also invite speakers and companies to showcase the latest technology to our DBM researchers.

Facility Hebelstrasse:

Confocal:

  • Confocal, Nikon A1R Nala
  • Confocal, Zeiss LSM 710 Rocky
  • Visitron CSU-W1 and Ablation laser, Thor

Widefield:

  • Nikon Ti Juerg
  • Olympus BX61 Diana
  • Olympus BX63 Apollo
  • Olympus IX50 Osiris
  • Olympus IX81 Sally
  • Olympus IX83

Other:

  • SlideScanner
  • Imagestream

Imaging PC:

  • IDEAS
  • Nikon Imaris
  • Olympus CellSens and CellP
  • SlideScan Analysis
  • Zen Imaris

Facility Mattenstrasse:

Confocal:

  • Confocal, Leica SP5
  • Confocal, Spinning Disk, Visitron

Widefield:

  • Leica DMI 4000
  • Leica DMi8
  • Leica Live Imaging Microscope DMi8
  • Nikon Eclipse E600
  • Zeiss Axio Imager Z2 Scanning Microscope
  • Zeiss Axio Imager Z1
  • Zeiss Axioskop

Stereo:

  • Leica Stereomicroscope MZ16FA
  • Nikon SMZ1500 Stereomicroscope

High content screening:

  • Operetta HCS Microscope

Other:

  • Zeiss Laser Capture Microscope

Imaging PC:

  • Imaging PC 1
  • Imaging PC 2

For further details on the systems or to book them please log in to our internal booking system.
https://iris.science-it.ch/auth/

Facility Hebelstrasse:

Dr. Mike Abanto
Department of Biomedicine/ University Hospital Basel
Hebelstrasse 20
4031 Basel
Switzerland

Tel: +41 (0)61 556 53 46

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Beat Erne
Departement of Biomedicine/ University of Basel
Klingelbergstrasse 50-70
4056 Basel
Switzerland
 

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.

Dr. Loïc Sauteur
Departement of Biomedicine/ University of Basel
Hebelstrasse 20
4031 Basel
Switzerland

Tel: +41 (0)61 328 55 53

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Facility Mattenstrasse:

Pascal Lorentz
Department of Biomedicine/ University of Basel
Mattenstrasse 28
4058 Basel
Switzerland

Tel: +41 (0)61 207 50 02
Fax: +41 (0)61 207 50 90

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General Information:
Before you start: Microscopy pitfalls:

http://jcb.rupress.org/content/172/1/9.full

Before you publish: Ethics and data manipulation, from JCB:

http://jcb.rupress.org/content/166/1/11.full

Sample preparation:

http://microscopy.duke.edu/sampleprep/if.html

https://www.google.ch/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0ahUKEwiVs5vD-pLWAhXIORQKHRtTA8wQFggnMAA&url=http%3A%2F%2Fwwwuser.gwdg.de%2F~uboehm%2Fimages%2F18.pdf&usg=AFQjCNHYOTjOjUFynC58vAd62RcL2-0SeQ

http://www.ihcworld.com/_protocols/general_ICC/fixation.htm

Mounting media:

http://www.uhnres.utoronto.ca/facilities/wcif/PDF/Mountants.pdf

Autofluorescence:

http://www.uhnres.utoronto.ca/facilities/wcif/PDF/Autofluorescence.pdf

Fluorochrome Table:

http://www.sciencegateway.org/resources/fae1.htm

Spectra Viewer:

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-Analysis/Labeling-Chemistry/Fluorescence-SpectraViewer.html

SVI Nyquist Calculator:

http://www.svi.nl/NyquistCalculator

General introduction to image analysis and automation in microscopy:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791844/

The following websites offer comprehensive learning for all aspects of microscopy and are a great resource:

http://microscopy.fsu.edu/primer/index.html
http://www.microscopyu.com/
http://www.olympusmicro.com/
http://www.olympusconfocal.com/theory/index.html
http://zeiss-campus.magnet.fsu.edu/
http://www.invitrogen.com/site/us/en/home/support/Tutorials.html
http://www.mikroskopie.de/ (German)

 

Software:
ImageJ: http://rsb.info.nih.gov/ij/download.html

Image J is a powerful open source image processing and analysis program.

There are a lot of plugins for all kind of purposes available.

Fiji: https://fiji.sc/ 

Fiji is an image processing package.

It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.

IrfanView: www.irfanview.net

IrfanView is a very fast, small, compact and innovative freeware (for non-commercial use) graphic viewer. (For PC only)

It contains a nice batch conversion (with image processing) to change picture formats and sizes. (e.g. tiff to jpg)

Automator:

Automator is a tool that is already included in the MAC operating system. It can also be used for batch conversion and for much more.

 

Video Tutorials:
ImageJ tutorials on youtube:

http://www.youtube.com/watch?v=KoqpCsha-UU

Cellprofiler on youtube:

http://www.youtube.com/results?search_query=cell+profiler&oq=cell+profiler&gs_l=youtube.3..0i10.204.2362.0.2515.13.13.0.0.0.0.115.1023.12j1.13.0...0.0...1ac.1.11.youtube.9-z6nDNvBkw

Imaris tutorials:

http://www.bitplane.com/go/knowledge-base/tutorial-videos

Introduction to confocal microscopy, Kurt Thorn:

http://www.youtube.com/user/ibioseminars/videos?query=microscopy

Introduction to fluorescence microscopy, Nico Sturman:

http://www.youtube.com/watch?list=SPAAAAED3D1EA9E4E1&feature=player_detailpage&v=iPrZ84kHH2U

Introduction to live cell, photoactivation, bleaching and super resolution, Jennifer Lippincott-Schwartz:

http://www.youtube.com/watch?feature=player_detailpage&v=FPCqvdsnJwQ

http://www.youtube.com/watch?feature=player_detailpage&v=bhjP9PqfJRE

http://www.youtube.com/watch?feature=player_detailpage&v=Bom9d-Knz0w

Introduction to super resolution imaging, Xiaowei Zhuang, Stefan Hell:

http://www.youtube.com/watch?feature=player_detailpage&v=w2Qo__sppcI

http://www.youtube.com/watch?feature=player_detailpage&v=DPGijjVTncs

http://www.youtube.com/watch?v=2NssL7RWmjc