Semi-automated

The Binary Pattern Dictionary Learning (BPDL) package is suitable for image analysis on a set/sequence of images to determine an atlas of a compact region. In particular, the application can be maping gene activation accross many samples, brain activations in a time domain, etc.

BIRL stands for "Benchmark on Image Registration methods with Landmark validation". BIRL is a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods.

Some key features of the framework:

• automatic execution of image registration of a sequence of image pairs
• integrated evaluation of registration performances using Target Registration Error (TRE)
• integrated visualization of performed registration
• running several image registration experiment in parallel
• resuming unfinished sequence of registration benchmark
• handling around dataset and creating own experiments
• rerun evaluation and visualisation for finished experiments

Collection of several basic standard image segmentation methods focusing on medical imaging. In particular, the key block/applications are (un)supervised image segmentation using superpixels, object centre detection and region growing with a shape prior. Besides the open-source code, there is also a few sample images.

Set of Tools for super resolution microscopy

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