VESCL: an open source 2D vessel contouring library.

PURPOSE: VESCL (pronounced 'vessel') is a novel vessel contouring library for computer-assisted 2D vessel contouring and segmentation. VESCL facilitates manual vessel segmentation in 2D medical images to generate gold-standard datasets for training, testing, and validating automatic vessel segmentation. METHODS: VESCL is an open-source C++ library designed for easy integration into medical image processing systems. VESCL provides an intuitive interface for drawing variable-width parametric curves along vessels in 2D images. It includes highly optimized localized filtering to automatically fit drawn curves to the nearest vessel centerline and automatically determine the varying vessel width along each curve. To support a variety of segmentation paradigms, VESCL can export multiple segmentation representations including binary segmentations, occupancy maps, and distance fields. RESULTS: VESCL provides sub-pixel resolution for vessel centerlines and vessel widths. It is optimized to segment small vessels with single- or sub-pixel widths that are visible to the human eye but hard to segment automatically via conventional filters. When tested on neurovascular digital subtraction angiography (DSA), VESCL's intuitive hand-drawn input with automatic curve fitting increased the speed of fully manual segmentation by 22× over conventional methods and by 3× over the best publicly available computer-assisted manual segmentation method. Accuracy was shown to be within the range of inter-operator variability of gold standard manually segmented data from a publicly available dataset of neurovascular DSA images as measured using Dice scores. Preliminary tests showed similar improvements for segmenting DSA of coronary arteries and RGB images of retinal arteries. CONCLUSION: VESCL is an open-source C++ library for contouring vessels in 2D images which can be used to reduce the tedious, labor-intensive process of manually generating gold-standard segmentations for training, testing, and comparing automatic segmentation methods.

Preliminary Results Comparing Thin Plate Splines with Finite Element Methods for Modeling Brain Deformation during Neurosurgery using Intraoperative Ultrasound.

Brain shift compensation attempts to model the deformation of the brain which occurs during the surgical removal of brain tumors to enable mapping of presurgical image data into patient coordinates during surgery and thus improve the accuracy and utility of neuro-navigation. We present preliminary results from clinical tumor resections that compare two methods for modeling brain deformation, a simple thin plate spline method that interpolates displacements and a more complex finite element method (FEM) that models physical and geometric constraints of the brain and its material properties. Both methods are driven by the same set of displacements at locations surrounding the tumor. These displacements were derived from sets of corresponding matched features that were automatically detected using the SIFT-Rank algorithm. The deformation accuracy was tested using a set of manually identified landmarks. The FEM method requires significantly more preprocessing than the spline method but both methods can be used to model deformations in the operating room in reasonable time frames. Our preliminary results indicate that the FEM deformation model significantly out-performs the spline-based approach for predicting the deformation of manual landmarks. While both methods compensate for brain shift, this work suggests that models that incorporate biophysics and geometric constraints may be more accurate.

Transient Bragg reflection gratings in erbium-doped fiber amplifiers.

A transient tunable Bragg reflection grating has been established in an erbium-doped fiber amplifier by the effect of a standing wave produced by counterpropagating cw light. Less than 1 mW of cw light was required to establish a grating with a 75% reflection coefficient at 1536 nm and an optical bandwidth (FWHM) of 16 MHz.Possible applications include dispersion compensation and dense wavelength-division multiplexing.