Data Storage and Analysis

    Data Storage

    The CIC offers data storage for large data sets.  The data storage server can be connected using iRods Explorer software, or via an internet browser.

    Connect using iRods Explorer

    Download iRods Explorer software for Windows environment here:

    iRods Explorer version 2.4d
    (right-click the link and select “Save link as…”)

    Settings needed for connection:

    • Host:
    • Zone: BIISA
    • Port: 1247

    CIC personnel will provide and user name and password.

    Data Processing and Analysis

    The CIC has three open access workstations. CIC staff can also process and analyze the data as a paid service.

    In-house Software

    • BioImageXD : Open source software for image processing, analysis and visualization
      BioImageXD is a collaborative open source software project, designed and developed by microscopists, cell biologists and programmers from the  universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG, Dresden, Germany, and collaborators worldwide. BioImageXD is a tool for the analysis and visualization of multidimensional biomedical images. It is designed for versatile and professional confocal image processing, covering e.g. 3D rendering and animation, colocalization analysis, accurate image adjustment, segmentation-based quantitative analyses and batch processing.
      The free software package is platform-independent, and can therefore be installed to computers running Windows, Linux, Mac OS etc.
      Free download from BioImageXD home page:
    • Flowing Software : Freeware software for flow cytometry data analysis (download it here).
      Flowing Software is a freeware flow cytometery data analysis software for Microsoft Windows environment. Flowing Software contains all regular data analysis capabilities. However, in addition to those, it has two additional goals:

      • To offer easy-to-use data analysis tools for high throughput analysis
      • To provide an environment for the implementation and development of new analysis algorithms.

    Other Software

    • NIS Elements : Nikon Eclipse offline licence
    • Zen : Zeiss LSM880 AiryScan offline licence
    • Bitplane Imaris 8.1: versatile data analysis and visualization software
    • AutoQuant : deconvolution software
    • ImageLab: free BioRad ChemiDoc offline software
    • IncuCyte 2018C: IncuCyte operating software
    • SlideBook 6 : 3i spinning disk data analysis software
    • FlowJo 10 : Flow cytometry analysis software
    • GelAnalyzer : Freeware gel analysis software
    • Fiji-ImageJ : Open source imaging software
    • Zen lite : Free tool for images taken with Zeiss LSM780
    • Neurolucida
    • Stereoinvestigator (MBF Bioscience)
    • Metamorph