Colocalisation analysis

Colocalization analysis
Co-localisation analysis

3D object based colocalisation

Submitted by Perrine on Fri, 02/22/2019 - 09:21

A user comes to the Facility: “I’ve got a set of 2 channels 3D images where objects are overlapping. I think the overlap might not be the same from object to object. I would like to quantify the physical overlap and get a map of quantifications”. Your mission: write the appropriate macro, knowing a user might always change her/his mind, and ask for more… Ready to take on the challenge ?


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
    • 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
need a thumbnail

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Icy SODA logo

Quote " finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc). "

Uses Gaussian-Mexican hat convolution for preprocessing.