3D ImageJ Suite

Boudier, Thomas
Ollion, Jean
Execution Platform
Implementation Type
Supported image dimension
Interaction Level

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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Last modified
04/27/2023 - 14:27