ISBI 2019 TUTORIAL on

GEODESIC METHODS FOR BIOMEDICAL IMAGE SEGMENTATION

Monday April 8th, 2019

 

Laurent D. Cohen   Directeur de Recherche au CNRS
CEREMADE, UMR CNRS 7534,
Université Paris Dauphine, PSL
Place du Marechal de Lattre de Tassigny
75775 Paris cedex 16, France
Tel. (33-1) 44 05 46 78 Fax (33-1) 44 05 45 99
Cohen @ ceremade.dauphine .fr
http://www.ceremade.dauphine.fr/~cohen

Postdoc : Open positions. Contact me.

 

link to DESCRIPTION OF the TUTORIAL

 

Tubular and tree structures appear very commonly in biomedical images like vessels, microtubules or neuron cells. Minimal paths have been used for long as an interactive tool to segment these structures as cost minimizing curves. The user usually provides start and end points on the image and gets the minimal path as output. These minimal paths correspond to minimal geodesics according to some adapted metric. They are a way to find a (set of) curve(s) globally minimizing the geodesic active contours energy. Finding a geodesic distance can be solved by the Eikonal equation using the fast and efficient Fast Marching method. Introduced first as a way to find the global minimum of a simplified active contour energy, we have recently extended these methods to cover all kinds of active contour energy terms. Also, various methods have been introduced that improve either the interactive aspects or their efficiency in order to make completely automatic or minimally interactive tools for image segmentation. For example, the metric can take into account both scale and orientation of the path. This leads to solving an anisotropic minimal path in a 2D or 3D+radius space (Figure 1). More recently, a new way to penalize the curvature in the framework of geodesic minimal paths was introduced, leading to more natural results in vessel extraction for example (Figure 2). In particular, much work has been applied to retina images like the automatic detection of vascular tree as well as the geometric analysis of these structures (Figure 3).

In this course we will present different methods based on geodesics from their basics to biomedical applications, in particular for blood vessel segmentation.

link to SLIDES

 

Some Papers to complete the tutorial:
 

• Initial Article on minimal paths
• Overview Article on first minimal paths
• Minimal paths: A book

 

• tubular Anisotropy
• FINSLER metrics : geodesics with curvature penalty
• FINSLER metrics : geodesics with region term

• Keypoints method

• Geodesic Voting

• Geodesic Voting 2

• minimal paths and virtual endoscopy

 

Some related subjects not presented in the tutorial:

• Fast extraction of tubular and tree 3D surfaces with front propagation methods.

• Fast Constrained Surface Extraction by Minimal Paths Similar paper in French
• Multiple contour finding and perceptual grouping using minimal paths
• Multiple Contour Finding and Perceptual Grouping as a set of Energy Minimizing Paths
• Geodesic re-meshing and parameterization using front propagation
• Landmark-based Computation for Heuristically Driven Path Planning.

 

Link to Numerical Tours on geodesic methods