Bradley M. Hemminger

Assessment of display performance for medical imaging systems

Digital imaging provides an effective means to electronically acquire, archive, distribute, and view medical images. Medical imaging display stations are an integral part of these operations. Therefore, it is vitally important to assure that electronic display devices do not compromise image quality and ultimately patient care. The AAPM Task Group 18 (TG18) recently published guidelines and acceptance criteria for acceptance testing and quality control of medical display devices. This paper is an executive summary of the TG18 report. TG18 guidelines include visual, quantitative, and advanced testing methodologies for primary and secondary class display devices. The characteristics, tested in conjunction with specially designed test patterns (i.e., TG18 patterns), include reflection, geometric distortion, luminance, the spatial and angular dependencies of luminance, resolution, noise, glare, chromaticity, and display artifacts. Geometric distortions are evaluated by linear measurements of the TG18-QC test pattern, which should render distortion coefficients less than 2%/5% for primary/secondary displays, respectively. Reflection measurements include specular and diffuse reflection coefficients from which the maximum allowable ambient lighting is determined such that contrast degradation due to display reflection remains below a 20% limit and the level of ambient luminance (Lamb) does not unduly compromise luminance ratio (LR) and contrast at low luminance levels. Luminance evaluation relies on visual assessment of low contrast features in the TG18-CT and TG18-MP test patterns, or quantitative measurements at 18 distinct luminance levels of the TG18-LN test patterns. The major acceptable criteria for primary/ secondary displays are maximum luminance of greater than 170/100 cd/m2, LR of greater than 250/100, and contrast conformance to that of the grayscale standard display function (GSDF) of better than 10%/20%, respectively. The angular response is tested to ascertain the viewing cone within which contrast conformance to the GSDF is better than 30%/60% and LR is greater than 175/70 for primary/secondary displays, or alternatively, within which the on-axis contrast thresholds of the TG18-CT test pattern remain discernible. The evaluation of luminance spatial uniformity at two distinct luminance levels across the display faceplate using TG18-UNL test patterns should yield nonuniformity coefficients smaller than 30%. The resolution evaluation includes the visual scoring of the CX test target in the TG18-QC or TG18-CX test patterns, which should yield scores greater than 4/6 for primary/secondary displays. Noise evaluation includes visual evaluation of the contrast threshold in the TG18-AFC test pattern, which should yield a minimum of 3/2 targets visible for primary/secondary displays. The guidelines also include methodologies for more quantitative resolution and noise measurements based on MTF and NPS analyses. The display glare test, based on the visibility of the low-contrast targets of the TG18-GV test pattern or the measurement of the glare ratio (GR), is expected to yield scores greater than 3/1 and GRs greater than 400/150 for primary/secondary displays. Chromaticity, measured across a display faceplate or between two display devices, is expected to render a u,v color separation of less than 0.01 for primary displays. The report offers further descriptions of prior standardization efforts, current display technologies, testing prerequisites, streamlined procedures and timelines, and TG18 test patterns.

Contrast Limited Adaptive Histogram Equalization image processing to improve the detection of simulated spiculations in dense mammograms

The purpose of this project was to determine whether Contrast Limited Adaptive Histogram Equalization (CLAHE) improves detection of simulated spiculations in dense mammograms. Lines simulating the appearance of spiculations, a common marker of malignancy when visualized with masses, were embedded in dense mammograms digitized at 50 micron pixels, 12 bits deep. Film images with no CLAHE applied were compared to film images with nine different combinations of clip levels and region sizes applied. A simulated spiculation was embedded in a background of dense breast tissue, with the orientation of the spiculation varied. The key variables involved in each trial included the orientation of the spiculation, contrast level of the spiculation and the CLAHE settings applied to the image. Combining the 10 CLAHE conditions, 4 contrast levels and 4 orientations gave 160 combinations. The trials were constructed by pairing 160 combinations of key variables with 40 backgrounds. Twenty student observers were asked to detect the orientation of the spiculation in the image. There was a statistically significant improvement in detection performance for spiculations with CLAHE over unenhanced images when the region size was set at 32 with a clip level of 2, and when the region size was set at 32 with a clip level of 4. The selected CLAHE settings should be tested in the clinic with digital mammograms to determine whether detection of spiculations associated with masses detected at mammography can be improved.

Assessment of display performance for medical imaging systems: Executive summary of AAPM TG18 report

Digital imaging provides an effective means to electronically acquire, archive, distribute, and view medical images. Medical imaging display stations are an integral part of these operations. Therefore, it is vitally important to assure that electronic display devices do not compromise image quality and ultimately patient care. The AAPM Task Group 18 (TG18) recently published guidelines and acceptance criteria for acceptance testing and quality control of medical display devices. This paper is an executive summary of the TG18 report. TG18 guidelines include visual, quantitative, and advanced testing methodologies for primary and secondary class display devices. The characteristics, tested in conjunction with specially designed test patterns (i.e., TG18 patterns), include reflection, geometric distortion, luminance, the spatial and angular dependencies of luminance, resolution, noise, glare, chromaticity, and display artifacts. Geometric distortions are evaluated by linear measurements of the TG18-QC test pattern, which should render distortion coefficients less than 2%/5% for primary/secondary displays, respectively. Reflection measurements include specular and diffuse reflection coefficients from which the maximum allowable ambient lighting is determined such that contrast degradation due to display reflection remains below a 20% limit and the level of ambient luminance (Lamb) does not unduly compromise luminance ratio (LR) and contrast at low luminance levels. Luminance evaluation relies on visual assessment of low contrast features in the TG18-CT and TG18-MP test patterns, or quantitative measurements at 18 distinct luminance levels of the TG18-LN test patterns. The major acceptable criteria for primary/ secondary displays are maximum luminance of greater than 170/100 cd/m2, LR of greater than 250/100, and contrast conformance to that of the grayscale standard display function (GSDF) of better than 10%/20%, respectively. The angular response is tested to ascertain the viewing cone within which contrast conformance to the GSDF is better than 30%/60% and LR is greater than 175/70 for primary/secondary displays, or alternatively, within which the on-axis contrast thresholds of the TG18-CT test pattern remain discernible. The evaluation of luminance spatial uniformity at two distinct luminance levels across the display faceplate using TG18-UNL test patterns should yield nonuniformity coefficients smaller than 30%. The resolution evaluation includes the visual scoring of the CX test target in the TG18-QC or TG18-CX test patterns, which should yield scores greater than 4/6 for primary/secondary displays. Noise evaluation includes visual evaluation of the contrast threshold in the TG18-AFC test pattern, which should yield a minimum of 3/2 targets visible for primary/secondary displays. The guidelines also include methodologies for more quantitative resolution and noise measurements based on MTF and NPS analyses. The display glare test, based on the visibility of the low-contrast targets of the TG18-GV test pattern or the measurement of the glare ratio (GR), is expected to yield scores greater than 3/1 and GRs greater than 400/150 for primary/secondary displays. Chromaticity, measured across a display faceplate or between two display devices, is expected to render a u,v color separation of less than 0.01 for primary displays. The report offers further descriptions of prior standardization efforts, current display technologies, testing prerequisites, streamlined procedures and timelines, and TG18 test patterns.

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits

UNLABELLEDnInvestigators conducting studies of the molecular genetics of complex traits in humans often need rationally to select a set of single nucleotide polymorphisms (SNPs) from the hundreds or thousands available for a candidate gene. Accomplishing this requires integration of genomic data from distributed databases and is both time-consuming and error-prone. We developed the TAMAL (Technology And Money Are Limiting) web site to help identify promising SNPs for further investigation. For a given list of genes, TAMAL identifies SNPs that meet user-specified criteria (e.g. haplotype tagging SNPs or SNP predicted to lead to amino acid changes) from current versions of online resources (i.e. HapMap, Perlegen, Affymetrix, dbSNP and the UCSC genome browser).nnnAVAILABILITYnTAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal.nnnSUPPLEMENTARY INFORMATIONnhttp://neoref.ils.unc.edu/tamal/.

A study of factors that affect the information-seeking behavior of academic scientists

In an effort to understand how academic scientists seek information relevant to their research in todays environment of ubiquitous electronic access, a correlation framework is built and regression analysis is applied to the survey results from 2,063 academic researchers in natural science, engineering, and medical science at five research universities in the United States. Previous work has reported descriptive statistics about these scientists information-seeking behavior. This study extends that work to examine relationships between scientists information-seeking behaviors and their personal and environmental factors. Several regression models, including the Poisson model, the logit model, and the ordered logit model, are built to interpret the correlation among scientists behaviors. In addition, exploratory factor analysis is used for data reduction. Overall, many factors were found to affect the specific information-seeking behaviors of scientists, including demographic, psychological, role-related, and environmental factors. Of the factors having an effect, academic position was the most important determinant of information behavior.

Mining connections between chemicals, proteins, and diseases extracted from Medline annotations

The biomedical literature is an important source of information about the biological activity and effects of chemicals. We present an application that extracts terms indicating biological activity of chemicals from Medline records, associates them with chemical name and stores the terms in a repository called ChemoText. We describe the construction of ChemoText and then demonstrate its utility in drug research by employing Swansons ABC discovery paradigm. We reproduce Swansons discovery of a connection between magnesium and migraine in a novel approach that uses only proteins as the intermediate B terms. We validate our methods by using a cutoff date and evaluate them by calculating precision and recall. In addition to magnesium, we have identified valproic acid and nitric oxide as chemicals which developed links to migraine. We hypothesize, based on protein annotations, that zinc and retinoic acid may play a role in migraine. The ChemoText repository has promise as a data source for drug discovery.

Decoupling the scholarly journal

Although many observers have advocated the reform of the scholarly publishing system, improvements to functions like peer review have been adopted sluggishly. We argue that this is due to the tight coupling of the journal system: the systems essential functions of archiving, registration, dissemination, and certification are bundled together and siloed into tens of thousands of individual journals. This tight coupling makes it difficult to change any one aspect of the system, choking out innovation. We suggest that the solution is the “decoupled journal (DcJ).” In this system, the functions are unbundled and performed as services, able to compete for patronage and evolve in response to the market. For instance, a scholar might deposit an article in her institutional repository, have it copyedited and typeset by one company, indexed for search by several others, self-marketed over her own social networks, and peer reviewed by one or more stamping agencies that connect her paper to external reviewers. The DcJ brings publishing out of its current seventeenth-century paradigm, and creates a Web-like environment of loosely joined pieces—a marketplace of tools that, like the Web, evolves quickly in response to new technologies and users needs. Importantly, this system is able to evolve from the current one, requiring only the continued development of bolt-on services external to the journal, particularly for peer review.

Mixture Modeling for Digital Mammogram Display and Analysis

We have devised a mammogram modeling system which greatly simplifies the development of, and can improve the accuracy and consistency of, computer-aided display and analysis algorithms for digital mammography. Our system segments the five major components of a mammogram: background, uncompressed-fat, fat, dense, and muscle. Differences in the amount and distribution of these components account for much of the variation between mammograms. Via segmentation, the corresponding variations are isolated; automated algorithms can consider the components independently or adapt their parameters based on component-specific statistics.

Assessment of Real-Time 3D Visualization for Cardiothoracic Diagnostic Evaluation and Surgery Planning

Rationale and ObjectivesRationale and Objectives: Three-dimensional (3D) real-time volume rendering has demonstrated improvements in clinical care for several areas of radiological imaging. We test whether advanced real-time rendering techniques combined with an effective user interface will allow radiologists and surgeons to improve their performance for cardiothoracic surgery planning and diagnostic evaluation.Material and MethodsMaterials and Methods: An interactive combination 3D and 2D visualization system developed at the University of North Carolina at Chapel Hill was compared against standard tiled 2D slice presentation on a viewbox. The system was evaluated for 23 complex cardiothoracic computed tomographic (CT) cases including heart–lung and lung transplantation, tumor resection, airway stent placement, repair of congenital heart defects, aortic aneurysm repair, and resection of pulmonary arteriovenous malformation. Radiologists and surgeons recorded their impressions with and without the use of the interactive visualization system.ResultsResults: The cardiothoracic surgeons reported positive benefits to using the 3D visualizations. The addition of the 3D visualization changed the surgical plan (65% of cases), increased the surgeon’s confidence (on average 40% per case), and correlated well with the anatomy found at surgery (95% of cases). The radiologists reported fewer and less major changes than the surgeons in their understanding of the case due to the 3D visualization. They found new findings or additional information about existing findings in 66% of the cases; however, they changed their radiology report in only 14% of the cases.ConclusionConclusion: With the appropriate choice of 3D real-time volume rendering and a well-designed user interface, both surgeons and radiologists benefit from viewing an interactive 3D visualization in addition to 2D images for surgery planning and diagnostic evaluation of complex cardiothoracic cases. This study finds that 3D visualization is especially helpful to the surgeon in understanding the case, and in communicating and planning the surgery. These results suggest that including real-time 3D visualization would be of clinical benefit for complex cardiothoracic CT cases.

A method for determination of optimal image enhancement for the detection of mammographic abnormalities

We present a paradigm for empirical evaluation of digital image enhancement algorithms for mammography that uses psychophysical methods for implementation and analysis of a clinically relevant detection task. In the experiment, the observer is asked to detect and assign to a quadrant, or indicate the absence of, a simulated mammographic structure characteristic of cancer embedded in a background image of normal breast tissue. Responses are indicated interactively on a computer workstation. The parameter values for the enhancement applied to the composite image may be varied on each trial, and structure detection performance is estimated for each enhancement condition. Preliminary investigations have provided insight into an appropriate viewing duration, and furthermore, suggest that nonradiologists may be used under this methodology for the tasks investigated thus far, for predicting parameter values for clinical investigation. We are presently using this method in evaluating several contrast enhancement algorithms of possible benefit in mammography. These methods enable an objective, clinically relevant evaluation, for the purpose of optimal parameter determination or performance assessment, of digital image-processing methods potentially used in mammography.