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Upcoming CIF Worshops PDF
Written by Yannick KREMPP   
Tuesday, 12 April 2016

Dear CIF users,

Please find below the program of the nex CIF workshops.


Limited places available, so make sure to register to Jean-Yves Chattons at  This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

Lectures will be given in english, and the students of the doctoral schools (neuroscience, FBM, etc.) can validate their participation to a workshop as one seminar for their credits. 

 The CIF Staff 

CZI Batch Converter for Axioscan Z1 users PDF
Written by Yannick KREMPP   
Tuesday, 12 April 2016


Many CIF users have trouble dealing with the CZI files endoded with JPEG XR from the slide scannner. Here's  a wrkflow you can use for your images:

Carl Zeiss offers a free software to handle CZI files acquired using the Zeiss Axioscan Z1 slide scanner.

It comes as a zipped folder. Just unpack it and use the "CZItoTIFFBatchConverter.exe" program.

Please read carefully the PDF manual included to understand how it works

Tested and working on Windows 7 X64 with default options. You can open the BigTIFF files in Photoshop, make your adjustements, and export them in whatever format you'd like from there.

 You can download it below or in the downloads section, as a registered user. 

Epalinges: Xenogen system back online PDF
Written by Yannick KREMPP   
Wednesday, 30 March 2016

Dear CIF users,

The Xenogen system located at the Epalinges campus is out of order until further notice.

We will update the status of the device here as soon as we have news to share, so please come back to check this page later.

Status update:

30.03.2016 : System down. Full check-up scheduled for tomorrow.

31.03.2016 : The check-up is planned for this afternoon at 13h30. We will let you know the status of the instrument afterwards.

Some users have asked about their bookings: they will off course be removed and you will not be charged for not using a device that malfunctioned

31.03.2016: (14h30) The system is up and running again. The camera cable has been slightly dislodged from its port, causing an error during the initialization.

Previous bookings have been removed.

Last Updated ( Thursday, 31 March 2016 )
2015-2016 Course: "Introduction to fluorescence imaging for the analysis of living cells" by J-Y. C. PDF
Written by Yannick KREMPP   
Sunday, 06 December 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 : Super-Resolution Microscopy !

- 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 ( Monday, 07 December 2015 )
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. 

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