Institute of Biomathematics and Biometry Mathematical Modelling in Ecology and Biosciences 3-D Image Display, Analysis and Evaluation

wd3d - A widget based 3-D display and evaluation program

Primarily for the analysis of signals from fluorescent in situ hybridization this program is used for display and analysis of 3-dimensional data sets. It is written under idl and can be used on all platforms idl runs on. Some C-written extensions of idl are added.

After loading the data set typically from a sequence of tiff-files the following processing steps are available:

• Display
  • Orthogonal section display by mouse interaction in the top left drawing regions.
  • Gallery display of selectable subvolume for inspection
  • Intensity profile display at chosen locations
  • Thresholded image display (see above top right drawing region)
  • Diverse histograms
  • Pseudo spatial representation (slicer)
• Segmentation
  • Manual or automatical selected threshold(s)
  • Labelling of connected components
  • Splitting of connected components interactively or automatically by various methods, e.g. watershed
  • Cleaning interactively or automatically by various methods, e.g. mathematical morphology opening and closing, size criteria
• Evaluation
  • Automatical count of fish signals by segmentation with 3-D top hat transform
  • Automatical count related to labeled components, e.g. the cell nuclei
  • Feature extraction of labeled components related to morphology and intensities
• Miscellaneous
  • Zooming and unzooming of the whole data set
  • Cutting down the data set to a sub-box
  • Selection of various parameters by mouse