Impact of chromophores on colour appearance in a computational skin model

Early diagnosis of skin cancer offers the patient more favorable treatment options. Color fidelity of skin images is a major concern for dermatologists as adoption of digital dermatoscopes is increasing rapidly. Accurate color depiction of the lesion and surrounding skin are vital in diagnostic evaluation of a lesion. We previously introduced VCT-Derma, a pipeline for dermatological Virtual Clinical Trials (VCTs) including detailed and flexible models of human skin and lesions, which represent the patient in the entire dermatoscopy-based diagnostic process. However, those initial models of skin and lesions did not properly account for tissue colors. Our new skin model accounts for tissue color appearance by incorporating chromophores (e.g., melanin, blood) into the tissue model, and simulating the optical properties of the various skin layers. The physical properties of the skin and lesion were selected from clinically plausible values. The model and simulated dermatoscope images were created in open modelling software, assuming a linear camera model. We have assumed ambient white lighting, with a 6mm distance to the camera. Our model of color appearance was characterised by comparing the brightness of the lesion to its depth. The brightness of the lesion is compared through the variability of the mean gray values of a cropped region around the lesion. We compare two skin models, one without extensive chromophore content and one with. Our preliminary evaluation of increasing chromophore content shows promise based on the results presented here. Further refinement and validation of the model is ongoing

Simulation pipeline for virtual clinical trials of dermatology images

We have designed a pipeline for developing Virtual Clinical Trials (VCTs) for optical imaging of skin lesions. Skin cancer is the most common cancer in the US; one in five Americans will develop it by the age of 70. Early diagnosis offers more favorable treatment options; currently available diagnostics, however, shows large reader-dependence. A simulation approach offers advantages in terms of the known ground truth and flexibility to model clinically observed lesion variability. The pipeline is motivated by our success with VCTs of breast imaging. Our open source pipeline has been used to develop and evaluate novel clinical-grade displays, a new generation of tomosynthesis systems, and search observer models. The proposed pipeline includes modules for the simulation of skin and subcutaneous tissue, insertion of lesion models, and simulated acquisition of optical images, followed by the virtual reading of simulated images and the analysis of task-based system performance. The physical properties of the skin and lesion were selected among clinically plausible values. Skin lesion images were simulated assuming the ambient white light, and a linear camera model. We have utilized the standards for optimal data representation based upon the XML schema, adopted from our breast imaging VCTs. The presentation describes VCT principles used for designing the pipeline. We present proof-of-concept results, and discuss the preliminary visual and quantitative evaluation. Integration of pipeline modules and its validation is ongoin

Effects of smartphone sensor characteristics on dermatoscopic images : a simulation study

Dermatoscopes are commonly used to evaluate skin lesions. The rising incidence of skin cancer has led to a wide array of medical imaging devices entering the market, some of which provide the patient the ability to analyze skin lesions themselves. They usually come in the form of smartphone attachments or mobile applications that leverage the optics of the smartphone to acquire the image; and in some cases, even give a preliminary diagnosis. In this digital age these devices look to ease the burden of having to visit a dermatologist multiple times. While these attachments are no doubt very useful, the image sensors used within smartphones are limited in terms of how much information they can process and effectively output to the user. Smartphone sensors are also very small which can result in a less detailed image as opposed to one from a professional camera. Our work is focused on the analysis of the information lost due to the known limitations of smartphone sensors, and its effect on the image appearance. This analysis has been performed using a virtual simulation pipeline for dermatology called VCT-Derma, which contains a module for a proprietary dermatoscope whose optical stack parameters will be adapted to the smartphone sensor specifications mentioned in this manuscript. This manuscript also describes the necessary sensor parameters required for adapting the simulation model, the software used along with any assumptions made, perceived differences in the resulting images, as well as the direction of the ongoing work

Adapting mathematical observer models for dermoscopy : a study

Purpose – Explore the possible use of mathematical observer models in dermoscopy. Methods – Mathematical Observers (MOs) have been used extensively in a Virtual Clinical Trial context as surrogates for human observers. They have commonly been used for radiology imaging to model lesion detection tasks, for e.g. in mammography and lung cancer screening. Increasingly reliable MOs have been researched that account for limitations of the human visual system (contrast sensitivity function and dynamic adaptation of the eye) as well as complex lesion characteristics and shapes (spiculations). State-of-the-art MOs, commonly used for radiology, have been applied to dermoscopy images and their usefulness and limitations explored. Results – Applying existing MO models, such as channelized hotelling observers, to dermoscopy is not straightforward and does not provide reliable results. Compared to radiology, dermoscopy images are color images so lesions are characterized by changes in color as opposed to intensity (as is the case for most state-of-the-art MO models). Little research has been performed on color MO models. In addition, skin lesions are complex and contain a wide range of features (e.g. globules, white veil, etc). An approach where a MO is trained to detect a single feature is not feasible. Instead, a novel architecture for a layered observer model is proposed, which contains a set of observer models, each targeting a feature/set of features. The individual observer outputs are then combined into an overall observer output. This can be applied to dermoscopy where human observer decisions are typically not based on the presence of individual lesion features, but rather by looking at overall lesion characteristics and presence or absence of groups of features. Conclusion – In this work we outline prior MO model work and explore usefulness and limitations for use in dermoscopy imaging, while exploring adaptations for making MOs better suitable for use in dermoscopy imaging

Data and script for Bayesian hierarchical model

Data are from questionnaire surveys conducted across tea estates in the landscape surrounding Kaziranga, Assam, Northeast India, on stakeholder attitudes towards the Asian elephant and its conservation. Script file is for assessing stakeholder attitudes while accounting for reporting error, using a Bayesian hierarchical model implemented in R and RStudio. Associated information is provided in Conservation Biology article titled 'A Bayesian hierarchical approach to quantifying stakeholder attitudes toward conservation in the presence of reporting error', authored by Divya Vasudev and Varun Goswami

Display systems for digital pathology : what are proper luminance, contrast and resolution settings?

The past few years digital pathology has been widely adopted. The display system is a crucial component in the overall digital pathology system, since pathologists decide based upon images visualized on the display. Quality of the display can influence clinical performance, but also workflow efficiency and ergonomics. Performance of radiology display systems has been extensively studied, and this resulted into standardization and clear requirements and guidelines. Digital pathology images and viewing conditions are very different compared to radiology. Fewer effort has gone in understanding what makes a digital pathology display fit for use, and there is no consensus yet in the digital pathology community about ideal specifications for digital pathology displays. This paper studies specific characteristics of digital pathology display systems, such as luminance, contrast and resolution. Effects of these characteristics on visibility of relevant pathological features is described, and recommendations are made for clinically meaningful levels of luminance, contrast and resolution

“In a tree by the brook, there’s a songbird who sings”: Woodlands in an agricultural matrix maintain functionality of a wintering bird community - Fig 2

<p><b>Predicted site-use of a) non-insectivorous guilds and b) insectivorous guilds as a function of vegetation and proximity effects as estimated through single-season occupancy models.</b> Predictions were model-averaged across all converged models; shaded regions represent associated standard errors. Covariates were standardized to have a mean of 0 and standard deviation of 1. Guilds where covariate effect has weak support are marked with an asterisk (‘*’). Guilds where covariate effect is unsupported are not included. Guild abbreviations: NEC (Nectarivores), GRN (Granivores), OMN (Omnivores), FRG (Frugivores), LHG (Large high-canopy gleaning insectivores), LUG (Large understory gleaning insectivores), LHS (Large high-canopy sallying insectivores), SMG (Small mid-canopy gleaning insectivores), SUG (Small understory gleaning insectivores), SMS (Small mid-canopy sallying insectivores), LWP (Large woodpeckers).</p

“In a tree by the brook, there’s a songbird who sings”: Woodlands in an agricultural matrix maintain functionality of a wintering bird community

<div><p>The agricultural matrix has increasingly been recognized for its potential to supplement Protected Areas (PAs) in biodiversity conservation. This potential is highly contextual, depending on composition and spatial configuration of matrix elements and their mechanistic relationship with biological communities. We investigate the effects of local vegetation structure, and proximity to a PA on the site-use of different guilds in a wintering bird community within the PA, and in wooded land-use types in the surrounding matrix. We used occupancy models to estimate covariate–guild relationships and predict site-use. We also compared species richness (estimated through capture–recapture models) and species naïve site-use between the PA and the matrix to evaluate taxonomic changes. We found that tree cover did not limit the site-use of most guilds of the community, probably due to high canopy cover across all chosen sites. Exceptions to this were guilds comprising generalist species. Shrub cover and bamboo cover had important effects on some woodland-associated guilds, suggesting a change in limiting factors for site-use under adequate tree cover. Site-use across the matrix was high for all analyzed guilds. This was found to be due to three non-exclusive reasons: (i) presence of one or more ubiquitous species (found all across the landscape) within some guilds, (ii) redundancy of species within guilds that buffered against a decrease in site-use, and (iii) turnover in guild composition/abundances to more generalist species from PA to matrix. Estimated species richness was higher in the matrix (107± 11; mean ± SE) than in the PA (90± 7), which may have been in part due to the addition of generalist species in the matrix. Understanding factors that limit biological communities is crucial to better managing the ever-increasing matrix for biodiversity conservation. Our study provides insights into the effects of different components of vegetation structure on the bird community in wooded land-use types in the matrix. We highlight the value of woodlands surrounding PAs in maintaining multiple guilds, and hence, the functionality of a wintering bird community. However, we caution that the matrix may fall short in retaining some specialized species of the community.</p></div