Rue du Bugnon 9, CH-1005, Lausanne, VD, Switzerland
+41 21 692 51 06 (Prof. J-Y. Chatton, Coordinator)
Contact :



Registration forms for the CIF platform

CIF Registration form (ver. 2024)
CIF > Imaris satellite license request form

    Guides and Manuals

    Documents written by the CIF staff or official manuals to operate our instruments.

    CIF Guides

    [All] Use of the Airyscan module on the Zeiss LSM 780-880 series

    How to correctly setup the Airyscan mode on Zeiss confocals for super-resolution. Written by Yannick Krempp

    [Bugnon] Zeiss LSM 780 User Manual

    Short user manual written by Yannick Krempp

    [Bugnon] Zeiss LSM 710 User Manual

    Short user manual written by Yannick Krempp

    [All] Zeiss Zen Multitrack setup for faster and cleaner acquisitions

    How to correctly setup multitrack channels using Zen on Zeiss confocals [710-780-880 series].

    Written by Yannick Krempp

    [Bugnon] Leica DMi8 User Guide

    Short user manual written by Yannick Krempp


      Official Manuals

      [All] Zeiss LSM 710,780 User Manual

      Official Zeiss Manual

      [Bugnon] Leica DMi8 Manual

      Official Leica Manual

        Free Software

        Free versions of commercial software and open-source packages used for image processing and analysis.

        Commercial Packages

        Brand Software OS Download page
        Zeiss Zen Lite | Zen Blue Edition 3.1 Windows
        Leica LAS X Core Offline Windows
        Nikon NIS Elements Viewer Windows, Mac OS X
        Hammamatsu NDP.View2 Windows, Mac OS X (Scroll down for links)
        Various (Adobe, Microsoft, Matlab,…) for academic UNIL users only Creative Cloud, Office, Matlab

        Open-source or Freeware Packages

        Author(s) Software OS Download page
        Eliceiri/LOCI group at the University of Wisconsin-Madison, and the Jug and Tomancak labs at the MPI-CBG in Dresden. Fiji (Image J + plugins)
        Windows, Mac OS X, Linux
        QuPath is developed at the University of Edinburgh. The software was originally created at the Centre for Cancer Research & Cell Biology at Queen’s University Belfast, as part of research projects funded by Invest Northern Ireland and Cancer Research UK. QuPath Windows, Mac OS X, Linux
        The CellProfiler project team is based in the Carpenter Lab  at the Broad Institute of Harvard and MIT. The project was started in 2003 by Anne E. Carpenter and Thouis (Ray) Jones in the Sabatini Laboratory (Whitehead Institute for Biomedical Research) and Golland laboratory (MIT’s CSAIL) and is actively improved and maintained. CellProfiler, Cellprofiler Analyst
        Windows, Mac OS X
        Orbit has been developed at Actelion Pharmaceuticals Ltd, now Idorsia Pharmaceuticals Ltd
        by Manuel Stritt.
        Orbit Windows, Mac OS X, Linux
        KNIME’s headquarters are based in Zurich, with additional offices in Konstanz, Berlin, and Austin. We’re open for innovation®, so visit us at KNIME. KNIME Analytics
        Windows, Mac OS X, Linux


        The CIF platform edits a yearly newsletter. Find here all the previous issues.

        CIF Newsletter 15 - October 2021
        Newsletter - November 2019
        Newsletter - June 2018

          Plugins, macros and scripts

          Plugins, macros and scripts written in various languages (java, python, macro) for extensible software like Fiji

          No downloads found!


            Workshop-related documents like slides, outlines or samples.

            Live Cell Imaging [Florence Morgenthaler, Luigi Bozzo, 2019]

            Critical steps and applications for live cell imaging in widefield & spinning disk confocal microscopy

            F-Techniques [Luigi Bozzo, 2019]

            Slides of the presentation given by Luigi Bozzo on the various advanced F-Techniques : FRAP, FCS, FRET, FLIM, principle and application.

            Using HRM for batch deconvolution [2019, Yannick KREMPP]

            Slides of the presentation given by Yannick Krempp on how to use the Huygens remote manager implemented at the CIF to do batch deconvolution.

            Deconvolution [2019, Arnaud Paradis]

            Slides from the CIF workshop given by Arnaud Paradis on Deconvolution