An Image Analysis Resource for Cancer Research: PIIP-Pathology Image Informatics Platform for Visualization, Analysis, and Management.

Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Thus far, new plugins have been developed and incorporated into the platform for out of focus detection, region of interest transformation, and IHC slide analysis. Our biomarker quantification and nuclear segmentation algorithms, written in MATLAB, have also been integrated into the viewer. This article describes the viewing software and the mechanism to extend functionality by plugins, brief descriptions of which are provided as examples, to guide users who want to use this platform. PIIP project materials, including a video describing its usage and applications, and links for the Sedeen Viewer, plug-ins, and user manuals are freely available through the project web page: http://pathiip.org Cancer Res; 77(21); e83-86. ©2017 AACR.

Probabilistic multi-shape segmentation of knee extensor and flexor muscles.

Patients with chronic obstructive pulmonary disease (COPD) often exhibit skeletal muscle weakness in lower limbs. Analysis of the shapes and sizes of these muscles can lead to more effective therapy. Unfortunately, segmenting these muscles from one another is a challenging task due to a lack of image information in many areas. We present a fully automatic segmentation method that overcomes the inherent difficulties of this problem to accurately segment the different muscles. Our method enforces a multi-region shape prior on the segmentation to ensure feasibility and provides an energy minimizing probabilistic segmentation that indicates areas of uncertainty. Our experiments on 3D MRI datasets yield an average Dice similarity coefficient of 0.92 +/- 0.03 with the ground truth.

Segmentation of intra-retinal layers from optical coherence tomography images using an active contour approach.

Optical coherence tomography (OCT) is a noninvasive, depth-resolved imaging modality that has become a prominent ophthalmic diagnostic technique. We present a semi-automated segmentation algorithm to detect intra-retinal layers in OCT images acquired from rodent models of retinal degeneration. We adapt Chan-Vese's energy-minimizing active contours without edges for the OCT images, which suffer from low contrast and are highly corrupted by noise. A multiphase framework with a circular shape prior is adopted in order to model the boundaries of retinal layers and estimate the shape parameters using least squares. We use a contextual scheme to balance the weight of different terms in the energy functional. The results from various synthetic experiments and segmentation results on OCT images of rats are presented, demonstrating the strength of our method to detect the desired retinal layers with sufficient accuracy even in the presence of intensity inhomogeneity resulting from blood vessels. Our algorithm achieved an average Dice similarity coefficient of 0.84 over all segmented retinal layers, and of 0.94 for the combined nerve fiber layer, ganglion cell layer, and inner plexiform layer which are the critical layers for glaucomatous degeneration.

Longitudinal study of retinal degeneration in a rat using spectral domain optical coherence tomography.

Rodent models of retinal degenerative diseases are used by vision scientists to develop therapies and to understand mechanisms of disease progression. Measurement of changes to the thickness of the various retinal layers provides an objective metric to evaluate the performance of the therapy. Because invasive histology is terminal and provides only a single data point, non-invasive imaging modalities are required to better study progression, and to reduce the number of animals used in research. Optical Coherence Tomography (OCT) has emerged as a dominant imaging modality for human ophthalmic imaging, but has only recently gained significant attention for rodent retinal imaging. OCT provides cross section images of retina with micron-scale resolution which permits measurement of the retinal layer thickness. However, in order to be useful to vision scientists, a significant fraction of the retinal surface needs to be measured. In addition, because the retinal thickness normally varies as a function of distance from optic nerve head, it is critical to sample all regions of the retina in a systematic fashion. We present a longitudinal study of OCT to measure retinal degeneration in rats which have undergone optic nerve axotomy, a well characterized form of rapid retinal degeneration. Volumetric images of the retina acquired with OCT in a time course study were segmented in 2D using a semi-automatic segmentation algorithm. Then, using a 3D algorithm, thickness measurements were quantified across the surface of the retina for all volume segmentations. The resulting maps of the changes to retinal thickness over time represent the progression of degeneration across the surface of the retina during injury. The computational tools complement OCT retinal volumetric acquisition, resulting in a powerful tool for vision scientists working with rodents.

Intra-retinal layer segmentation in optical coherence tomography using an active contour approach.

Optical coherence tomography (OCT) is a non-invasive, depth resolved imaging modality that has become a prominent ophthalmic diagnostic technique. We present an automatic segmentation algorithm to detect intra-retinal layers in OCT images acquired from rodent models of retinal degeneration. We adapt Chan-Vese's energy-minimizing active contours without edges for OCT images, which suffer from low contrast and are highly corrupted by noise. We adopt a multi-phase framework with a circular shape prior in order to model the boundaries of retinal layers and estimate the shape parameters using least squares. We use a contextual scheme to balance the weight of different terms in the energy functional. The results from various synthetic experiments and segmentation results on 20 OCT images from four rats are presented, demonstrating the strength of our method to detect the desired retinal layers with sufficient accuracy and average Dice similarity coefficient of 0.85, specifically 0.94 for the the ganglion cell layer, which is the relevant layer for glaucoma diagnosis.