Data Analysis

Extracting quantitative data from a scientific image is a critical step in obtaining usable information. The facility offers several software packages running on powerful workstations. Contact the staff for training and access.


  • Bitplane Imaris: a popular, sophisticated and versatile package best known for 3D rendering and volumetric analysis functions. Filament tracing available.
  • SVI Hyugens: deconvolution package to increase the spatial resolution of microscopic images. Note that deconvolution requires images acquired at unusually high sampling density, 40 nm in xy and 200 nm in z. Widefield, spinning disk and point scanner images options.
  • Zeiss Zen Black and Blue: full-feature Zeiss package to analyze confocal images
  • Nikon Elements: full license of the Nikon software for off-line analysis
  • Fiji: a custom distribution of ImageJ specifically designed for light microscopy images. Unlike other software, Fiji is open-source and can be freely downloaded and used. A versatile and popular option for image analysis, ImageJ has a large community of users and an impressive amount of plugins that extends its functionality. Among many available resources, the MIC staff provides an extensive computer class on Fiji each Spring.  


The facility operates two high-end workstations with image analysis software. These computers must be reserved on the calendar before use.

  • Workstation 1 / GD931B
    Dell Precision 5810: Intel Xeon E5-1650 processor, 128 GB of RAM, AMD Radeon 390 graphics card, 500 GB SSD (Windows), 4 TB spinning hard drive (data)
    Software: Zeiss Zen Black, Zen Blue, Nikon Elements, Bitplane Imaris, ImageJ
  • Workstation 2 / GD922
    Dell Precision 5810: Intel Xeon E5-2687W processor, 128 GB of RAM, Nvidia GForce 1080 graphics card, 500 GB SSD (Windows), 16 TB raid 1 spinning drive array (data)
    Software: Zeiss Zen Black, Zen Blue, SVI Hyugens, ImageJ.
    (Workstation 2 is connected to the Zeiss Airyscan system with a dedicated 10 Gbps link and should be used to store and process Airyscan images.)
Workstation 1 in the lab.
Workstation 1 / GD931B
Workstation 2 in the lab.
Workstation 2 / GD922
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