V-Mail: 3D-Enabled Correspondence about Spatial Data on (Almost) All Your Devices.

We present V-Mail, a framework of cross-platform applications, interactive techniques, and communication protocols for improved multi-person correspondence about spatial 3D datasets. Inspired by the daily use of e-mail, V-Mail seeks to enable a similar style of rapid, multi-person communication accessible on any device; however, it aims to do this in the new context of spatial 3D communication, where limited access to 3D graphics hardware typically prevents such communication. The approach integrates visual data storytelling with data exploration, spatial annotations, and animated transitions. V-Mail "data stories" are exported in a standard video file format to establish a common baseline level of access on (almost) any device. The V-Mail framework also includes a series of complementary client applications and plugins that enable different degrees of story co-authoring and data exploration, adjusted automatically to match the capabilities of various devices. A lightweight, phone-based V-Mail app makes it possible to annotate data by adding captions to the video. These spatial annotations are then immediately accessible to team members running high-end 3D graphics visualization systems that also include a V-Mail client, implemented as a plugin. Results and evaluation from applying V-Mail to assist communication within an interdisciplinary science team studying Antarctic ice sheets confirm the utility of the asynchronous, cross-platform collaborative framework while also highlighting some current limitations and opportunities for future work.

Signature maps for automatic identification of prostate cancer from colorimetric analysis of H&E- and IHC-stained histopathological specimens.

Prostate cancer (PCa) is a major cause of cancer death among men. The histopathological examination of post-surgical prostate specimens and manual annotation of PCa not only allow for detailed assessment of disease characteristics and extent, but also supply the ground truth for developing of computer-aided diagnosis (CAD) systems for PCa detection before definitive treatment. As manual cancer annotation is tedious and subjective, there have been a number of publications describing methods for automating the procedure via the analysis of digitized whole-slide images (WSIs). However, these studies have focused only on the analysis of WSIs stained with hematoxylin and eosin (H&E), even though there is additional information that could be obtained from immunohistochemical (IHC) staining. In this work, we propose a framework for automating the annotation of PCa that is based on automated colorimetric analysis of both H&E and IHC WSIs stained with a triple-antibody cocktail against high-molecular weight cytokeratin (HMWCK), p63, and α-methylacyl CoA racemase (AMACR). The analysis outputs were then used to train a regression model to estimate the distribution of cancerous epithelium within slides. The approach yielded an AUC of 0.951, sensitivity of 87.1%, and specificity of 90.7% as compared to slide-level annotations, and generalized well to cancers of all grades.

Microstructure Imaging of Crossing (MIX) White Matter Fibers from diffusion MRI.

Diffusion MRI (dMRI) reveals microstructural features of the brain white matter by quantifying the anisotropic diffusion of water molecules within axonal bundles. Yet, identifying features such as axonal orientation dispersion, density, diameter, etc., in complex white matter fiber configurations (e.g. crossings) has proved challenging. Besides optimized data acquisition and advanced biophysical models, computational procedures to fit such models to the data are critical. However, these procedures have been largely overlooked by the dMRI microstructure community and new, more versatile, approaches are needed to solve complex biophysical model fitting problems. Existing methods are limited to models assuming single fiber orientation, relevant to limited brain areas like the corpus callosum, or multiple orientations but without the ability to extract detailed microstructural features. Here, we introduce a new and versatile optimization technique (MIX), which enables microstructure imaging of crossing white matter fibers. We provide a MATLAB implementation of MIX, and demonstrate its applicability to general microstructure models in fiber crossings using synthetic as well as ex-vivo and in-vivo brain data.