Fitting tree model with CNN and geodesics to track vesselsand application to Ultrasound Localization Microscopy data

Segmentation of tubular structures in vascular imaging is a well studied task, although it is rare that we try to infuse knowledge of the tree-like structure of the regions to be detected. Our work focuses on detecting the important landmarks in the vascular network (via CNN performing both localization and classification of the points of interest) and representing vessels as the edges in some minimal distance tree graph. We leverage geodesic methods relevant to the detection of vessels and their geometry, making use of the space of positions and orientations so that 2D vessels can be accurately represented as trees. We build our model to carry tracking on Ultrasound Localization Microscopy (ULM) data, proposing to build a good cost function for tracking on this type of data. We also test our framework on synthetic and eye fundus data. Results show that scarcity of well annotated ULM data is an obstacle to localization of vascular landmarks but the Orientation Score built from ULM data yields good geodesics for tracking blood vessels.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

Chan-Vese Attention U-Net: An attention mechanism for robust segmentation

When studying the results of a segmentation algorithm using convolutional neural networks, one wonders about the reliability and consistency of the results. This leads to questioning the possibility of using such an algorithm in applications where there is little room for doubt. We propose in this paper a new attention gate based on the use of Chan-Vese energy minimization to control more precisely the segmentation masks given by a standard CNN architecture such as the U-Net model. This mechanism allows to obtain a constraint on the segmentation based on the resolution of a PDE. The study of the results allows us to observe the spatial information retained by the neural network on the region of interest and obtains competitive results on the binary segmentation. We illustrate the efficiency of this approach for medical image segmentation on a database of MRI brain images

Deformable Voxel Grids for Shape Comparisons

We present Deformable Voxel Grids (DVGs) for 3D shapes comparison and processing. It consists of a voxel grid which is deformed to approximate the silhouette of a shape, via energy-minimization. By interpreting the DVG as a local coordinates system, it provides a better embedding space than a regular voxel grid, since it is adapted to the geometry of the shape. It also allows to deform the shape by moving the control points of the DVG, in a similar manner to the Free Form Deformation, but with easier interpretability of the control points positions. After proposing a computation scheme of the energies compatible with meshes and pointclouds, we demonstrate the use of DVGs in a variety of applications: correspondences via cubification, style transfer, shape retrieval and PCA deformations. The first two require no learning and can be readily run on any shapes in a matter of minutes on modest hardware. As for the last two, they require to first optimize DVGs on a collection of shapes, which amounts to a pre-processing step. Then, determining PCA coordinates is straightforward and brings a few parameters to deform a shape

An Application of CLP: Checking the Correctness of Theorems in Geometry

International audienceConstraint Logic Programming can be advantageously used to deal with quadratic constraints stemming from the verification of planar geometry theorems. A hybrid symbolic--numeric representation involving radicals and multiple precision rationals is used to denote the results of quadratic equations. A unification--like algorithm tests for the equality of two expressions using that representation. The proposed approach also utilizes geometric transformations to reduce the number of quadratic equations defining geometric constructions involving circles and straight lines. A large number (512) of geometry theorems has been verified using the proposed approach. Those theorems had been proven correct using a significantly more complex (exponential) approach in a treatise authored by Chou in 1988. Even though the proposed approach is based on verification -rather than strict correctness utilized by Chou- the efficiency attained is polynomial thus making the approach useful in classroom situations where a construction attempted by student has to be quickly validated or refuted