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Biomedical Imaging Group

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Deformable Models for the Segmentation of Biomedical Images

Anaïs Badoual, Biomedical Imaging Group (BIG), EPFL, Switzerland

We propose here a collection of Icy plugins for biomedical image segmentation.

Locally Refinable Snake

This plugin implements fast active contours for biomedical image segmentation. Through the interface, one can locally increases the degrees of freedom of the curves. It allows to catch details of intricate shapes.

Reference: A. Badoual, D. Schmitter, M. Unser, "Locally Refinable Parametric Snakes," IEEE International Conference on Image Processing (ICIP'15), 2015.
Texture Snake

This plugin implements active contours to segment structures with similar intensity distribution and low contrast with the background. They are trained on-the-fly from small collections of pixels provided by the user. Their parametric representation allows for an intuitive manipulation of the curves through control points.

Reference: A. Badoual, M. Unser, A. Depeursinge, "Texture-Driven Parametric Snakes for Semi-Automatic Image Segmentation," Computer Vision and Image Understanding, 2019.
Active Tessellation

This plugin implements active contours to segment cell aggregates. They are robust to membrane gaps and to high levels of noise. Their subdivision-based representation allows for an intuitive manipulation of the curves through control points.

Reference: A. Badoual, A. Galan, D. Sage, and M. Unser, "Deforming tessellations for the segmentation of cell aggregates," IEEE International Symposium on Biomedical Imaging (ISBI'19), 2019.
Subdivision Snake

This plugin implements fast active contours for biomedical image segmentation. They adapt the resolution of their curve to the level of details of their target. Their subdivision-based representation allows for an intuitive manipulation of the curves through control points.

Reference: A. Badoual, D. Schmitter, V. Uhlmann, M. Unser, "Multiresolution Subdivision Snakes," IEEE Transactions on Image Processing, 2017.
Active Subdivision Surface

This plugin implements active surfaces to segment biomedical volumes They adapt the resolution of their curve to the level of details of their target. Their subdivision-based representation allows for an intuitive manipulation of the curves through control points.

Reference: A. Badoual, P. Novara, L. Romani, D. Schmitter, and M. Unser, "A Non-Stationary Subdivision Scheme for the Construction of Deformable Models with Sphere-Like Topology," Graphical Models, 2017.