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ATHENA server scheduled maintenance PDF
Written by Yannick KREMPP   
Monday, 30 May 2016

Dear CIF Users,

The ATHENA file server will be shut down and unreachable on Friday, June the 10th, the whole day.

If you plan to use the CIF resources this particular day, please make sure you bring your own storage solution (USB hard drive, flashdrive, etc..) or that you have access to another network location. Do not store your files locally.

We apologize for the inconvenience,


The CIF Staff. 

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 )
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