connected components

Description

This suite provides plugins to enhance 3D capabilities of ImageJ.

  • 3D Filters (mean, median, max, min, tophat, max local, …) and edge and symmetry filter
  • 3D Segmentation (iterative thresholding, spots segmentation, watershed, …)
    • 3D hysteresis thresholding with two thresholds (see 2D hysteresis for explanation).
    • 3D simple segmentation with thresholding to label 3D objects (similar to 3D objects counter).
    • 3D iterative thresholding (find optimal threshold for each object).
    • 3D spot segmentation with various local threshold estimations.
    • 3D Maxima Finder (with noise parameter)
    • 3D seeds-based watershed with automatic local maxima detection for seeds.
  • 3D Mathematical Morphology tools (fill holes, binary closing, distance map, …)
  • 3D RoiManager (3D display and analysis of 3D objects)
  • 3D Analysis (Geometrical measurements, Mesh measurements, Convex hull, …)
    • 3D Geometrical measurements (volume, surface, …) for each labelled object.
    • 3D Centroid, to compute centroids of labelled objects.
    • 3D Intensity measurements (mean, integrated density, …) in a opened image for each labelled object.
    • 3D Shape measurements (compactness, elongation, …) for each labelled object.
    • 3D Mesh Measurements after triangulation (see 3D Viewer for surface mesh computation).
    • 3D fitting by an ellipsoid and main direction computation (details here).
    • 3D convex hull (see http://rsbweb.nih.gov/ij/plugins/3d-convex-hull/index.html).
    • 3D Radial Distance Area Ratio (RDAR)
    • 3D Density, to compute density of dots, based on closest distance analysis (details here).
  • 3D MereoTopology (Relationship between objects)
  • 3D Tools (Drawing ellipsoids and lines, cropping, …)
    • Drawing 3D line
    • Drawing 3D ellipsoids in any direction
    • Drawing in stacks as volumes
    • Drawing in 3D viewer as surfaces
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Description

FracLac is for digital image analysis. Use it to measure difficult to describe morphological features.
FracLac is a plugin for ImageJ. It is freely available software developed and maintained by our lab at the School of Community Health, Faculty of Science, Charles Sturt University, Australia. The author of the software and project lead is also the author of this document (me, Audrey Karperien). The basic box counting algorithm was originally modified from ImageJ's box counting algorithm and H. Jelinek's NIH Image plugin, and was further elaborated based on extensive research and development. The convex hull algorithm was provided by Thomas Roy, University of Alberta, Canada. As open source software, with the continuing help of a host of users and collaborators, FracLac has evolved to a suite of fractal analysis and morphology functions.

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Description

Simple workflow description for ImageJ, step-by-step description for delineating focal adhesions, count and characterize their positions.  

Measurement of dynamics is not involved.