Colocalisation analysis

Colocalization analysis
Co-localisation analysis

SMLM is a mature but still growing field, which still lacks efficient and user-friendly analysis and visualization software platform adapted for both users and developers. We here introduce PoCA, a powerful open-source software platform dedicated to the visualization and analysis of 2D and 3D point-cloud data. PoCA allows manipulating large datasets, and integrates a plugin architecture, a native batch analysis engine and a Python code interpreter, facilitating both the analysis of data and the integration of new methods.

Visualization, segmentation and exploration of 3D SMLM data

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