Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

/pdf/fiji-an-open-source-platform-for-biological-image-analysis-1v529iu3cx.pdf

Fiji: an open-source platform for biological-image analysis

A snake is an energy-minimizing spline guided by external constraint forces and influenced by image forces that pull it toward features such as lines and edges. Snakes are active contour models: they lock onto nearby edges, localizing them accurately. Scale-space continuation can be used to enlarge the capture region surrounding a feature. Snakes provide a unified account of a number of visual problems, including detection of edges, lines, and subjective contours; motion tracking; and stereo matching. We have used snakes successfully for interactive interpretation, in which user-imposed constraint forces guide the snake near features of interest.

/pdf/snakes-active-contour-models-2cuxgoykah.pdf

Snakes : Active Contour Models

We propose a new model for active contours to detect objects in a given image, based on techniques of curve evolution, Mumford-Shah (1989) functional for segmentation and level sets. Our model can detect objects whose boundaries are not necessarily defined by the gradient. We minimize an energy which can be seen as a particular case of the minimal partition problem. In the level set formulation, the problem becomes a "mean-curvature flow"-like evolving the active contour, which will stop on the desired boundary. However, the stopping term does not depend on the gradient of the image, as in the classical active contour models, but is instead related to a particular segmentation of the image. We give a numerical algorithm using finite differences. Finally, we present various experimental results and in particular some examples for which the classical snakes methods based on the gradient are not applicable. Also, the initial curve can be anywhere in the image, and interior contours are automatically detected.

/pdf/active-contours-without-edges-2tt3qz9lq0.pdf

Active contours without edges

An automated method for segmenting magnetic resonance head images into brain and non-brain has been developed. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of MR sequences. The method, Brain Extraction Tool (BET), uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre-processing before being applied. We describe the new method and give examples of results and the results of extensive quantitative testing against "gold-standard" hand segmentations, and two other popular automated methods.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.10062

Fast robust automated brain extraction

https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf

Cortical surface-based analysis. I. Segmentation and surface reconstruction

Constraints on deformable models: recovering 3D shape and nongrid motion

Spacetime constraints are a new method for creating character animation. The animator specifies what the character has to do, for instance, "jump from here to there, clearing a hurdle in between;" how the motion should be performed, for instance "don't waste energy," or "come down hard enough to splatter whatever you land on;" the character's physical structure---the geometry, mass, connectivity, etc. of the parts; and the physical resources' available to the character to accomplish the motion, for instance the character's muscles, a floor to push off from, etc. The requirements contained in this description, together with Newton's laws, comprise a problem of constrained optimization. The solution to this problem is a physically valid motion satisfying the "what" constraints and optimizing the "how" criteria. We present as examples a Luxo lamp performing a variety of coordinated motions. These realistic motions conform to such principles of traditional animation as anticipation, squash-and-stretch, follow-through, and timing.

Spacetime constraints

Oriented patterns, such as those produced by propagation, accretion, or deformation, are common in nature and therefore an important class for visual analysis. Our approach to understanding such patterns is to decompose them into two parts: the flow field, describing the direction of anisotropy; and the residual pattern obtained by describing the image in a coordinate system built from the flow field. We develop a method for the local estimation of anisotropy and a method for combining the estimates to construct a flow coordinate system. Several examples of the use of these methods are presented. These include the use of the flow coordinates to provide preferred directions for edge detection, detection of anomalies, fitting simple models to the straightened pattern, and detecting singularities in the flow field.

Analyzing oriented patterns

The creation of believable and endearing characters in computer graphics presents a number of technical challenges, including the modeling, animation and rendering of complex shapes such as heads, hands, and clothing. Traditionally, these shapes have been modeled with NURBS surfaces despite the severe topological restrictions that NURBS impose. In order to move beyond these restrictions, we have recently introduced subdivision surfaces into our production environment. Subdivision surfaces are not new, but their use in high-end CG production has been limited. Here we describe a series of developments that were required in order for subdivision surfaces to meet the demands of high-end production. First, we devised a practical technique for constructing provably smooth variable-radius fillets and blends. Second, we developed methods for using subdivision surfaces in clothing simulation including a new algorithm for efficient collision detection. Third, we developed a method for constructing smooth scalar fields on subdivision surfaces, thereby enabling the use of a wider class of programmable shaders. These developments, which were used extensively in our recently completed short film Geri’s game, have become a highly valued feature of our production environment. CR Categories: I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling; I.3.3 [Computer Graphics]: Picture/Image Generation.

/pdf/subdivision-surfaces-in-character-animation-21z0zbwppn.pdf

Michael Kass

Papers

Snakes : Active Contour Models

Constraints on deformable models: recovering 3D shape and nongrid motion

Spacetime constraints

Analyzing oriented patterns

Subdivision surfaces in character animation