FluoCells #1 BPAE cells, image by Sarah Swanson
FluoCells #3 mouse kidney

NIC Image Analysis

Analysis & Processing Software:

Free or Open-Source

  • FIJI

    FIJI (ImageJ, with plug-ins) is Java-based software for working with image data and is available for all operating systems. Its plug-ins cover an extensive range of imaging needs, including:

    • Manipulation of images, time lapse, Z stacks and color
    • Annotation, including scale and time
    • 3-D modeling and visualization
    • Quantitative analysis of image properties such as intensity, particle measurement and tracking, colocalization etc.

    FIJI is used and maintained by an extensive range of imaging scientists and professionals.

  • GIMP

    GIMP is a free and powerful alternative to Adobe Photoshop with versions available for most operating systems.

  • Danuser Lab MATLAB Software

    MATLAB packages from the Danuser lab

    • uTrack 2.0: Sophisticated particle tracking algorithm
    • Biosensor Processing: Automated analysis and generation of heat maps from ratiometric biosensor data
    • QFSM: Speckle analysis of actin, tubulin polymerization
    • cmeAnalysis: Quantifies clathrin-coated pit dynamics from time-lapse data
    • plusTipTracker: Tracks many microtubule parameters using +TIP marker live cell imaging
    • ClusterTrack: Works with plusTipTracker to allow analysis of microtubules using only +TIP imaging
  • BisQue Image Analysis Environment

    BisQue (Bio-Image Semantic Query User Environment) allows you to store, visualize, organize and analyze images in the cloud. BisQue was developed for the exchange and exploration of biological images, but can support image data from other domains.

  • CellProfiler

    CellProfiler is a machine learning-based tool for automated and quantitative analysis of high-throughput data sets (e.g., high volume fluorescent phenotype screens). It is very good at segmentation (nucleus, PM, cytoplasm) of cells in culture and tissues.

Data Management & Analysis Software:

Available free to UW-Madison Students, Faculty, and Staff.

UW-Madison login required.

Micrographs of plant cells