Main Title
Recommanded Seminar PDF
Written by Yannick KREMPP   
Wednesday, 18 November 2015

Dear CIF users,

Professor Alain Chedotal will give a seminar on the analysis of tranparent tissues at the DNF. Topics such as tissue clarification and ultramicroscopy will be part of this talk.

As the CIF now provides access to this type of equipment (Epalinges platform), we highly recommand those interested in the use of our ultramicroscope to attend to this seminar.


  Thursday, November 26th at 12:15  in the Petit Auditoire of the DNF
rue du Bugnon 9.

“3D Analysis of Axon Guidance in Transparent Vertebrate Embryos” 

Prof. Alain Chédotal

INSERM, Institut de la Vision, Paris, France



Over the past few years, many tissue clearing techniques have been developed to clear mouse brains, thereby preserving three-dimensional structure but their complexity has limited their use. We showed recently (Belle et al., 2014) that immunolabeling of axonal tracts followed by optical clearing with solvents (3DISCO) and light sheet microscopy reveals brain connectivity in mouse embryos and post-natal brains. This method can be used to rapidly screen and describe axon guidance defects in knockout mice. Using appropriate antibodies and software, the number of neurons within specific brain nuclei can be easily and rapidly counted in 3D. We have also adapted this technique to vertebrate embryos from many vertebrate species such as Xenopus, birds or reptiles. I will illustrate how this method facilitates the analysis axon guidance and, using commissural neurons as a model system. I will also present a project aimed at providing the first comprehensive description of neuronal development in human embryos during the first trimester of gestation.


Belle, M., Godefroy, D., Dominici, C., Heitz-Marchaland, C., Zelina, P., Hellal, F., Bradke, F. and Chédotal, A. (2014) A Simple Method for 3D Analysis of Immunolabeled Axonal Tracts in a Transparent Nervous System. Cell Reports 9: 1191-1201.


To access the DNF, please use preferentially public transportation ( If however you need to drive your car, please come a little before the beginning of the seminar, so that the DNF can provide you with a temporary parking permit. 

Latest CIF Newsletter available PDF
Written by Yannick KREMPP   
Friday, 09 October 2015

The latest newsletter has arrived !


Make sure to grab a copy here:

CIF Newsletter 2015

 The CIF Staff 

Last Updated ( Friday, 09 October 2015 )
2015-2016 Course: "Introduction to fluorescence imaging for the analysis of living cells" by J-Y. C. PDF
Written by Yannick KREMPP   
Tuesday, 18 August 2015

 2015-2016 CIF COURSES


Cours de privat docent & Cellular Imaging Facility (CIF) 
Dr  Jean-Yves CHATTON 
 Introduction to fluorescence imaging for the analysis of living cells
Place: Petit Auditoire de l'Ecole de Médecine, rue du Bugnon 9 (1er étage)
Schedule: Winter Semester – Tuesdays    12:15 – 14:00
5 January 2016 : Basics of transmitted light and fluorescence microscopy
12 January 2016 : Confocal microscopy 
19 January 2016 : Modes of image formation, acquisition, signal sampling
26 January 2016 : Dynamic recording of cellular functions by fluorescence imaging.
Intracellular ion imaging and cellular signaling.
Problems related to imaging of living cells
2 February 2016 : Other optical applications (topics to be announced):

- lectures will be given in English.
- in parallel with theoretical lectures, demonstrations will be proposed on the confocal microscopes of the Cellular Imaging Facility (details and registration on site).
- gives right to ONE credit for students of doctoral schools (FBM and neuroscience)
Admission to the course is free and open to anyone interested
(Please register  to This e-mail address is being protected from spam bots, you need JavaScript enabled to view it  -- on site registration possible


Last Updated ( Tuesday, 18 August 2015 )
Nikon SMZ 25 Stereomicroscope at the Bugnon and Dorigny campus PDF
Written by Yannick KREMPP   
Monday, 06 July 2015

The CIF recently acquired some new stereomicroscopes for the Bugnon and Dorigny campus to replace the old Leica stereomicroscopes.

Before going into the details of what these new setups are capable of, it can be useful to know that the old stereomicroscopes will remain available but only as a mean to quickly check some samples as they are now stripped off of their computers. Without any acquisition device attached, these old Leica setups are also put outside of the booking system.

Now with this topic behind us, here's a short list of the features available on the new systems:


Both setups come with the following features:


  • A 25:1 zoom range with a 3.15x up to 315x magnification through the eyepieces, depending on the objective used.
  • 1x and 2x Plan Apo Objectives
  • Stereo and Macro modes
  • Illumination for both Brightfield and Fluorescence
  • Motorized zoom, focus shutters and filters 
  • NIS Basic Research acquisition software that allows Single, Multichannel, Z-Stacks, Video, Time-Lapse and Extended Depth of Focus acquisitions (or any combination of that)
  • Nikon's brand new DsRi2 color camera with a 16.25 Megapixels Full Frame CMOS sensor for ultra high image quality.



The Bugnon setup has some nice additions:


  • A fully motorized stage
  • An optional Polarizing attachment
  • The ability to acquire both multi-position and tiled (mosaics) images. 




 Image done with SMZ 25 using the Extended Depth of Focus (Yannick Krempp)

If you plan to use on of this setup, please request a training to either Arnaud Paradis or Yannick Krempp.

The CIF Staff

Last Updated ( Monday, 06 July 2015 )
Ultramicroscopy at CIF Epalinges: The CIF offers now the possibility to do light-sheet microscopy PDF
Written by Yannick KREMPP   
Tuesday, 23 June 2015

The CIF offers now the possibility to do light-sheet microscopy with the Light Sheet UltraMicroscope II from LaVisionBioTec which has recently been installed at CIF Epalinges.

Imaging large samples into the depth of the tissue needs certain procedures to reduce the opacity. The tissue has to be virtually transparent. Some samples like Zebra Fish are mostly transparent by nature but the majority of samples are opaque. This counteracts all attempts to image the sample in total. Nowadays, two main principles of creating translucent samples called clearing procedures have been established (either using organic solvent or aqueous buffer). Thank to its transparent properties, the sample can then be imaged very deeply with a light sheet microscope.

Light sheet fluorescence microscopy is a fluorescence microscopy technique with good optical sectioning capabilities and reasonably high speed. In contrast to epifluorescence microscopy only a thin slice of the sample is illuminated (by the light sheet) perpendicularly to the direction of observation.



A few technical facts about the system currently installed: 

  • The UltraMicroscope II has a bidirectional triple light sheet technology.
  • This technology allows to generate 6 focused light sheets to excite samples from the side while the fluorescence light is detected by a sCMOS camera perpendicular to the illumination plane.
  • The dynamic horizontal light sheet focus guarantees excellent Z-resolution covering the entire field of view.
  • Moving the sample through the light sheet generates a 3D image stack. Selective excitation of the focal plane reduces bleaching and photo toxicity significantly.
  • The open setup allows the analysis of cleared samples in any clearing solution (organic solvent or aqueous buffer) or in vivo data acquisition in aqueous media.
  • The sample size can vary from mm3 up to 1 cm3. Different working distances also contribute to better image large samples into the depth of the tissue.
  • Four lasers light sources (405 nm, 488 nm, 561 nm and/or a 640 nm laser) are available to adapt to your own applications.
  • The combination of a 2x objective together with a zoom allows variable magnification from to 1.26 to 12.6x.
  • Higher magnification objectives will be added soon.


If you plan to use this system, or just have some questions relative to the science behind it, please ask Florence Morgenthaler at the CIF Epalinges.

You can also find more information about that technology right here:


Last Updated ( Tuesday, 23 June 2015 )
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