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

NIC Image Analysis

Analysis & Processing Software:

Free or Open-Source

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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 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 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.

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Adobe Photoshop & Lightroom

UW-Madison has a federated login for Adobe Creative Cloud applications including Photoshop (digital image editing) and Lightroom (digital image database). Check the Campus Software Library for more info.

Google Drive & Box Cloud Storage

UW-Madison has cloud storage on Google Drive or Box. Go to wisc.edu and select “My UW” from the top menu to find these options.

Microsoft Office 365: Excel and Powerpoint

Microsoft Office can be installed for free on your personal computer if you have a UW-Madison login. Check the Campus Software Library for more info.

Micrographs of plant cells