User-selected Regions Research Articles

Beyond RGB: A Spectral Image Processing Software Application for Cultural Heritage Studio Photography

A software application for colorimetric and spectral processing of six-channel spectral images has recently been developed. The application, called Beyond RGB, takes as input two RAW RGB image sets (object/flat-field/dark current) captured under two different lighting or filtering conditions, and outputs 1.) a color managed RGB image with ancillary information about the accuracy of the color calibration and 2.) a spectral reflectance transform that enables the interactive estimation of reflectance curves from user-selected regions of interest in the image. Beyond RGB was designed with considerations for form, function, and user friendliness, and is intended for use by cultural heritage imaging professionals. It is cross-platform compatible and is operated through an interactive graphical user interface. Beyond RGB is a living, updatable, open-source project, and is freely available for download from the project’s public GitHub repository.

A New Technique for Century-Scale Wind Component Indices

Advancing the understanding of how variations in the climate over the ocean influences the weather over the United States can be aided by developing marine climatic indices. Herein, wind component indices are developed using nearly 125 years of wind observations from ships. A new technique using probability density functions for the values of meridional and zonal wind components is developed to create indices for a user-selected region and accumulation interval (e.g., annual or seasonal) over a climatological period. The index is a measure of the shift in the likelihood of values above or below a threshold for a given season or year as compared to the long-term (e.g., 125 year) probability distribution. The new index method is demonstrated using ship-based wind observations for select regions of the Atlantic Ocean. Ship observations are extracted from release 3.0.0 of the International Comprehensive Ocean-Atmosphere Data Set. Prior to index creation, an assessment of wind data quality is completed, and suspect observations are removed. The method to create a probabilistic wind component index is described along with a metric of the uncertainty in the calculated index. Two wind component indices, for regions in the north Atlantic and eastern Gulf of Mexico, are presented to demonstrate the technique. Using the Gulf of Mexico index as a case study, we compare the wind component indices to precipitation measured over the Gulf coastal states and identify several relationships between multi-year changes in winds in the eastern Gulf of Mexico and precipitation on a seasonal basis. Exploring the spatiotemporal patterns of the onshore/offshore component wind indices derived from seasonal wind forecasts could provide a metric for future prediction of seasonal or annual precipitation to support the agricultural sector. The index method demonstrated can be applied to other spatiotemporal regions for different parameters and using other source datasets.

New robust method for image copyright protection using histogram features and Sine Cosine Algorithm

Zero-watermarking methods are widely used for efficient copyright protection of digital images. These methods have the ability to withstand both common image processing attacks and some geometric attacks. However, they cannot effectively resist the complex image attacks such as translation, cropping, combined geometric attacks, UnZign, etc. For this purpose, we propose in this work a novel robust zero-watermarking method that can effectively resist several complex image attacks. The proposed method involves the use of the histogram descriptor to generate a secret sequence of binary values from a user-selected Region of Interest (ROI). In order to check the intellectual property rights, the Sine Cosine Algorithm (SCA) is used for detecting the ROI in the attacked image. Then, the computed histogram of this ROI is binarized with a secret method. Next, the resulting sequence of binary values is compared to the original one generated from the original ROI. If there is a high similarity between these binary sequences, the grayscale image copyrights are validated. The simulation results show that the proposed method is not only resistant to geometric attacks (rotation, scaling) and to common image attacks (JPEG compression, filtering, etc.), but it is also robust against the most complex image attacks (cropping, translation, combined geometric attacks, etc.). Furthermore, the results of the comparisons carried out in terms of robustness against different types of attacks prove the superiority of our method over other similar recent zero-watermarking methods.

Intuitive Transfer Function Editing Using Relative Visibility Histograms

In this paper, we present an interactive approach for intuitively editing colors and opacity values in transfer functions for volume visualization. We introduce the concept of a relative visibility histogram, which represents the difference between the global visibility distribution across the full volume and the local visibility distribution within a user-selected region in the viewport. From this measure, we can infer what subset of the 3D volume the user intends to select when they click on a region in the 2D rendered image of the data set, and use this to modify relevant parts of the transfer function. We use this selection mechanism for two alternative purposes. The first is to allow output-driven editing of the transfer function, whereby a user can change the opacity values and colors of features without directly having to manipulate the transfer function itself. The second is to extract visually dominant features in any user-selected region of interest, so that the user may individually edit their appearance and then merge these to create new transfer functions. Our approach is lightweight compared to similar techniques and performs in real-time.

Digital image analysis as an aid in the assessment of the combined positive score in ovarian carcinoma.

e14584 Background: Developing scoring methods for PD-L1 to identify patients who will respond effectively to anti-PD1 therapy is key in the development of companion and complementary diagnostic assays. The Combined Positive Score (CPS) is an elegant method for the evaluation of PD-L1 expression in solid tumors. CPS includes the number of PD-L1 positive cells (tumor, lymphocytes and macrophages) in relation to total tumor cells. The accurate manual capturing of total number of tumor cells can be a challenge to pathologists. Methods: Image analysis was used to evaluate possibledifferences in tumor density for well, moderately, and poorly differentiated ovarian epithelial serious carcinomas. Multiple regions of interest of 158 hematoxylin-stained specimens were analyzed. Algorithm parameters were systematically adjusted to minimize mean differences in tumor count relative to manually counted scores in small, user-selected regions of 33 representative specimens. Results: The average nuclei count ranged between 2000 and 7000 with ~50% falling between 4.0-5.5 x 103. Conclusions: Digital image analysis of nuclear quantification has been shown to be a useful tool to aid the pathologist with the correct assessment of the CPS score.

Pre-clinical validation of virtual bronchoscopy using 3D Slicer

Lung cancer still represents the leading cause of cancer-related death, and the long-term survival rate remains low. Computed tomography (CT) is currently the most common imaging modality for lung diseases recognition. The purpose of this work was to develop a simple and easily accessible virtual bronchoscopy system to be coupled with a customized electromagnetic (EM) tracking system for navigation in the lung and which requires as little user interaction as possible, while maintaining high usability. The proposed method has been implemented as an extension to the open-source platform, 3D Slicer. It creates a virtual reconstruction of the airways starting from CT images for virtual navigation. It provides tools for pre-procedural planning and virtual navigation, and it has been optimized for use in combination with a [Formula: see text] of freedom EM tracking sensor. Performance of the algorithm has been evaluated in ex vivo and in vivo testing. During ex vivo testing, nine volunteer physicians tested the implemented algorithm to navigate three separate targets placed inside a breathing pig lung model. In general, the system proved easy to use and accurate in replicating the clinical setting and seemed to help choose the correct path without any previous experience or image analysis. Two separate animal studies confirmed technical feasibility and usability of the system. This work describes an easily accessible virtual bronchoscopy system for navigation in the lung. The system provides the user with a complete set of tools that facilitate navigation towards user-selected regions of interest. Results from ex vivo and in vivo studies showed that the system opens the way for potential future work with virtual navigation for safe and reliable airway disease diagnosis.

Use of Ultrasound Echotexture Analysis to Determine the Presence of Nonalcoholic Fatty Liver Disease

Introduction: It would be desirable to identify a non-invasive method for determining whether and how much fat there is in the liver. Ultrasound imaging has been used for this purpose using descriptive measures. This study aims to evaluate whether raw ultrasound radiofrequency data, using echotexture of a region of interest in the liver is a valid, quantitative tool for assessing fatty liver. Methods: We applied an echotexture technique of ultrasound images to fatty livers in an attempt to determine the presence of fat in the liver. Previous work has shown that the echotexture of ultrasound images of fatty livers are different from normal livers. The echotexture can be quantified using the probability distribution of echo intensities obtained from a Nakagami distribution, defined by a parameter, ‘M', which can be used as a surrogate measure of the underlying echotexture. Increased values of M indicate fibrofatty infiltration. In this study, the raw ultrasound radiofrequency data from individuals with no previous diagnosis of fatty liver disease were acquired by a trained sonographer. The images were analyzed offline using custom software to generate an M parameter from a user-selected region of interest in the liver. The same images were also evaluated by a trained radiologist who graded them as “normal”, “mild” or “moderate” fatty liver. Results: Images from 24 sequentially-recruited subjects were used. Of these, 14 were classified by the radiologist as “normal”, 5 were “mild”, and 5 were “moderate”. None had “severe” fatty liver. The M-parameter for the “normal” group was 0.703 ± 0.068; for the “mild” group was 0.798± 0.032; and for the “moderate” group was 0.796± 0.018. The differences between the “normal” group and the combined group with mild or moderate fatty liver were significant (p < 0.00018). Using a threshold of 0.76, normal livers and livers with mild or moderate fatty infiltration could be separated with 100% sensitivity and 85.7% specificity, with an area under the curve of 0.94. Conclusion: Individuals without fatty liver have significantly different ultrasound echotexture of liver than those who do. Preliminary evidence indicates that ultrasound echotexture analysis may provide a quick, noninvasive alternative method to reliably determine the presence of fatty liver. Currently we are not able to distinguish among the levels of severity with significant probability. The results reported here need to be confirmed in a larger patient sample.

GT-Scan: identifying unique genomic targets

A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome editing or regulatory interference. Specificity, however, is a major problem, and the targeted locus must be chosen with care to avoid inadvertently affecting other loci ('off-targets') in the genome. To address this we have created 'Genome Target Scan' (GT-Scan), a flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have. GT-Scan gives the user flexibility to define the desired characteristics of targets and off-targets via a simple 'target rule', and its interactive output allows detailed inspection of each of the most promising candidate targets. GT-Scan can be used to identify optimal targets for CRISPR/Cas systems, but its flexibility gives it potential to be adapted to other genome-targeting technologies as well. GT-Scan can be run via the web at: http://gt-scan.braembl.org.au.

Consed: a graphical editor for next-generation sequencing

The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added. The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html dgordon@uw.edu .

An analysis of tropical cyclone occurrence in the Southern Hemisphere derived from a new satellite-era data set

Satellite remote sensing is vital to accurately estimate tropical cyclone (TC) parameters such as position and intensity. A TC archive for the Southern Hemisphere (SH) has been prepared for the ‘satellite era’, and it now consists of best track data, covering name (and/or unique identification number), position and intensity (in terms of central pressure). Based on these best track data, TC climatologies for the South Indian Ocean (SIO) and South Pacific Ocean (SPO) are investigated. Variability in TC activity is examined depending on different phases of the El Niño-Southern Oscillation (ENSO). The outcomes demonstrate prospects for improving the regional seasonal prediction of TC activity. The growth in the availability of satellite data is found to have a significant influence on the quantity and quality of available TC data, particularly in relation to the intensity of TCs. To provide a means of accessing detailed information and data on historical TCs in the SH, a specialized website for disseminating results and data was developed using the OpenLayers platform. This allows dynamic map navigation of detailed information for user-selected regions.

Stereo-video inpainting

As the production of stereoscopic content increases, so does the need for post-production tools for that content. Video inpainting has become an important tool for rig removal, but there has been little consideration of the problem in stereo. We present an algorithm for stereo-video inpainting that builds on existing exemplar-based video completion and also considers the issues of view consistency. Given user-selected regions in the sequence, which may be in the same location in several frames and in both views, the objective is to fill in this area using all the available picture information. Existing algorithms lack temporal consistency, causing flickering and other artifacts. We explore the use of long-term picture information across many frames in order to achieve temporal consistency at the same time as exploiting inter-view dependencies within the same framework.

Multivariate statistics applications in phase analysis of STEM-EDS spectrum images

Spectrum imaging (SI) methods are displacing traditional spot analyses as the predominant paradigm for spectroscopic analysis with electron beam instrumentation. The multivariate nature of SI provides clear advantages for qualitative analysis of multiphase specimens relative to traditional gray-scale images acquired with non-spectroscopic signals, where different phases with similar average atomic number may exhibit the same intensity. However, with the improvement in qualitative analysis with the SI paradigm has come a decline in the quantitative analysis of the phases thus identified, since the spectra from individual pixels typically have insufficient counting statistics for proper quantification. The present paper outlines a methodology for quantitative analysis within the spectral imaging paradigm, which is illustrated through X-ray energy-dispersive spectroscopy (EDS) of a multiphase (Pb,La)(Zr,Ti)O 3 ceramic in scanning transmission electron microscopy (STEM). Statistical analysis of STEM-EDS SI is shown to identify the number of distinct phases in the analyzed specimen and to provide better segmentation than the STEM high-angle annular dark-field (HAADF) signal. Representative spectra for the identified phases are extracted from the segmented images with and without exclusion of pixels that exhibit spectral contributions from multiple phases, and subsequently quantified using Cliff–Lorimer sensitivity factors. The phase compositions extracted with the method while excluding pixels from multiple phases are found to be in good agreement with those extracted from user-selected regions of interest, while providing improved confidence intervals. Without exclusion of multiphase pixels, the extracted composition is found to be in poor statistical agreement with the other results because of systematic errors arising from the cross-phase spectral contamination. The proposed method allows quantification to be performed in the presence of discontinuous phase distributions and overlapping phases, challenges that are typical of many nanoscale analyses performed by STEM-EDS.

NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation

The calculation of contact-dependent secondary structure propensity (CSSP) is a unique and sensitive method that detects non-native secondary structure propensities in protein sequences. This method has applications in predicting local conformational change, which typically is observed in core sequences of protein aggregation and amyloid fibril formation. NetCSSP implements the latest version of the CSSP algorithm and provides a Flash chart-based graphic interface that enables an interactive calculation of CSSP values for any user-selected regions in a given protein sequence. This feature also can quantitatively estimate the mutational effect on changes in native or non-native secondary structural propensities in local sequences. In addition, this web tool provides precalculated non-native secondary structure propensities for over 1 400 000 fragments that are seven-residues long, collected from PDB structures. They are searchable for chameleon subsequences that can serve as the core of amyloid fibril formation. The NetCSSP web tool is available at http://cssp2.sookmyung.ac.kr/.

Root gravitropism in response to a signal originating outside of the cap.

We have developed image analysis software linked to a rotating stage, allowing constraint of any user-selected region of a root at a prescribed angle during root gravitropism. This device allows the cap of a graviresponding root to reach vertical while maintaining a selected region within the elongation zone at a gravistimulated angle. Under these conditions gravitropic curvature of roots of Zea mays L. continues long after the root cap reaches vertical, indicating that a signal from outside of the cap can contribute to the curvature response.

Work in progress: ultrasonic texture of normal rat liver tissue using a standardized in vivo measurement.

A prototype computer-augmented diagnostic ultrasound system was used in an investigation of the range of echo amplitudes obtained from measurements of normal exteriorized rat livers. A secondary goal was to develop a method for minimizing variations in measurement techniques and instrument stability. The average echo amplitude was obtained from a user-selected homogeneous region of the liver on a B-mode scan image. A similar B-mode scan of a commercially available liver tissue equivalent phantom was also obtained immediately after each rat liver measurement and was used as a calibration scan. A normalization factor developed from the calibration scan was used to correct all in vivo measurements for system variation. The average echo amplitude from the livers of a group of normal rats, when corrected by the calibration scan, exhibited a narrow range of values with a coefficient of variation of only 5%. The development of a technique that yields a narrow range of values for normal tissues should encourage further investigation of tissue characterization methods.