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PURPOSE: The Medical Imaging and Data Resource Center (MIDRC) was created to facilitate medical imaging machine learning (ML) research for tasks including early detection, diagnosis, prognosis, and assessment of treatment response related to the coronavirus disease 2019 pandemic and beyond. The purpose of this work was to create a publicly available metrology resource to assist researchers in evaluating the performance of their medical image analysis ML algorithms. APPROACH: An interactive decision tree, called MIDRC-MetricTree, has been developed, organized by the type of task that the ML algorithm was trained to perform. The criteria for this decision tree were that (1) users can select information such as the type of task, the nature of the reference standard, and the type of the algorithm output and (2) based on the user input, recommendations are provided regarding appropriate performance evaluation approaches and metrics, including literature references and, when possible, links to publicly available software/code as well as short tutorial videos. RESULTS: Five types of tasks were identified for the decision tree: (a) classification, (b) detection/localization, (c) segmentation, (d) time-to-event (TTE) analysis, and (e) estimation. As an example, the classification branch of the decision tree includes two-class (binary) and multiclass classification tasks and provides suggestions for methods, metrics, software/code recommendations, and literature references for situations where the algorithm produces either binary or non-binary (e.g., continuous) output and for reference standards with negligible or non-negligible variability and unreliability. CONCLUSIONS: The publicly available decision tree is a resource to assist researchers in conducting task-specific performance evaluations, including classification, detection/localization, segmentation, TTE, and estimation tasks.

Purpose To investigate the combination of mammography radiomics and quantitative three-compartment breast (3CB) image analysis of dual-energy mammography to limit unnecessary benign breast biopsies. Materials and Methods For this prospective study, dual-energy craniocaudal and mediolateral oblique mammograms were obtained immediately before biopsy in 109 women (mean age, 51 years; range, 31-85 years) with Breast Imaging Reporting and Data System category 4 or 5 breast masses (35 invasive cancers, 74 benign) from 2013 through 2017. The three quantitative compartments of water, lipid, and protein thickness at each pixel were calculated from the attenuation at high and low energy by using a within-image phantom. Masses were automatically segmented and features were extracted from the low-energy mammograms and the quantitative compartment images. Tenfold cross-validations using a linear discriminant classifier with predefined feature signatures helped differentiate between malignant and benign masses by means of (a) water-lipid-protein composition images alone, (b) mammography radiomics alone, and (c) a combined image analysis of both. Positive predictive value of biopsy performed (PPV3) at maximum sensitivity was the primary performance metric, and results were compared with those for conventional diagnostic digital mammography. Results The PPV3 for conventional diagnostic digital mammography in our data set was 32.1% (35 of 109; 95% confidence interval [CI]: 23.9%, 41.3%), with a sensitivity of 100%. In comparison, combined mammography radiomics plus quantitative 3CB image analysis had PPV3 of 49% (34 of 70; 95% CI: 36.5%, 58.9%; P < .001), with a sensitivity of 97% (34 of 35; 95% CI: 90.3%, 100%; P < .001) and 35.8% (39 of 109) fewer total biopsies (P < .001). Conclusion Quantitative three-compartment breast image analysis of breast masses combined with mammography radiomics has the potential to reduce unnecessary breast biopsies. © RSNA, 2018 Online supplemental material is available for this article.

BACKGROUND. In human lupus nephritis (LN), tubulointerstitial inflammation (TII) on biopsy predicts progression to endstage renal disease (ESRD). However, only about half of patients with moderate-to-severe TII develop ESRD. We hypothesized that this heterogeneity in outcome reflects different underlying inflammatory states. Therefore, we interrogated renal biopsies from LN longitudinal and cross-sectional cohorts. METHODS. Data were acquired using conventional and highly multiplexed confocal microscopy. To accurately segment cells across whole biopsies, and to understand their spatial relationships, we developed computational pipelines by training and implementing several deep-learning models and other computer vision techniques. RESULTS. High B cell densities were associated with protection from ESRD. In contrast, high densities of [CD8.sup.+], yo, and other CD4CD8- T cells were associated with both acute renal failure and progression to ESRD. B cells were often organized into large periglomerular neighborhoods with Tfh cells, while [CD4.sup.-] T cells formed small neighborhoods in the tubulointerstitium, with frequency that predicted progression to ESRD. CONCLUSION. These data reveal that specific in situ inflammatory states are associated with refractory and progressive renal disease. FUNDING. This study was funded by the NIH Autoimmunity Centers of Excellence (AI082724), Department of Defense (LRI180083), Alliance for Lupus Research, and NIH awards (S10-OD025081, S10-RR021039, and P30-CA14599)., Introduction For over 50 years, systemic lupus erythematosus has been thought to result from a break in systemic tolerance and production of pathogenic autoreactive antibodies (1, 2). This canonical model [...]

Evaluation of segmentation algorithms usually involves comparisons of segmentations to gold-standard delineations without regard to the ultimate medical decision-making task. We compare two segmentation evaluations methods-a Dice similarity coefficient (DSC) evaluation and a diagnostic classification task-based evaluation method using lesions from breast computed tomography. In our investigation, we use results from two previously developed lesion-segmentation algorithms [a global active contour model (GAC) and a global with local aspects active contour model]. Although similar DSC values were obtained (0.80 versus 0.77), we show that the global + local active contour (GLAC) model, as compared with the GAC model, is able to yield significantly improved classification performance in terms of area under the receivers operating characteristic (ROC) curve in the task of distinguishing malignant from benign lesions. [Area under the [Formula: see text] compared to 0.63, [Formula: see text]]. This is mainly because the GLAC model yields better detailed information required in the calculation of morphological features. Based on our findings, we conclude that the DSC metric alone is not sufficient for evaluating segmentation lesions in computer-aided diagnosis tasks.

We present and evaluate a method for the three-dimensional (3-D) segmentation of breast masses on dedicated breast computed tomography (bCT) and automated 3-D breast ultrasound images. The segmentation method, refined from our previous segmentation method for masses on contrast-enhanced bCT, includes two steps: (1) initial contour estimation and (2) active contour-based segmentation to further evolve and refine the initial contour by adding a local energy term to the level-set equation. Segmentation performance was assessed in terms of Dice coefficients (DICE) for 129 lesions on noncontrast bCT, 38 lesions on contrast-enhanced bCT, and 98 lesions on 3-D breast ultrasound (US) images. For bCT, DICE values of 0.82 and 0.80 were obtained on contrast-enhanced and noncontrast images, respectively. The improvement in segmentation performance with respect to that of our previous method was statistically significant ( p = 0.002 ). Moreover, segmentation appeared robust with respect to the presence of glandular tissue. For 3-D breast US, the DICE value was 0.71. Hence, our method obtained promising results for both 3-D imaging modalities, laying a solid foundation for further quantitative image analysis and potential future expansion to other 3-D imaging modalities.

Dedicated breast CT (bCT) produces high-resolution 3D tomographic images of the breast, fully resolving fibroglandular tissue structures within the breast and allowing for breast lesion detection and assessment in 3D. In order to enable quantitative analysis, such as volumetrics, automated lesion segmentation on bCT is highly desirable. In addition, accurate output from CAD (computer-aided detection/diagnosis) methods depends on sufficient segmentation of lesions. Thus, in this study, we present a 3D lesion segmentation method for breast masses in contrast-enhanced bCT images. The segmentation algorithm follows a two-step approach. First, 3D radial-gradient index segmentation is used to obtain a crude initial contour, which is then refined by a 3D level set-based active contour algorithm. The data set included contrast-enhanced bCT images from 33 patients containing 38 masses (25 malignant, 13 benign). The mass centers served as input to the algorithm. In this study, three criteria for stopping the contour evolution were compared, based on (1) the change of region volume, (2) the average intensity in the segmented region increase at each iteration, and (3) the rate of change of the average intensity inside and outside the segmented region. Lesion segmentation was evaluated by computing the overlap ratio between computer segmentations and manually drawn lesion outlines. For each lesion, the overlap ratio was averaged across coronal, sagittal, and axial planes. The average overlap ratios for the three stopping criteria ranged from 0.66 to 0.68 (dice coefficient of 0.80 to 0.81), indicating that the proposed segmentation procedure is promising for use in quantitative dedicated bCT analyses.

PurposeTo investigate whether biologic image composition of mammographic lesions can improve upon existing mammographic quantitative image analysis (QIA) in estimating the probability of malignancy.MethodsThe study population consisted of 45 breast lesions imaged with dual-energy mammography prior to breast biopsy with final diagnosis resulting in 10 invasive ductal carcinomas, 5 ductal carcinomain situ, 11 fibroadenomas, and 19 other benign diagnoses. Analysis was threefold: (1) The raw low-energy mammographic images were analyzed with an established in-house QIA method, "QIA alone," (2) the three-compartment breast (3CB) composition measure-derived from the dual-energy mammography-of water, lipid, and protein thickness were assessed, "3CB alone", and (3) information from QIA and 3CB was combined, "QIA + 3CB." Analysis was initiated from radiologist-indicated lesion centers and was otherwise fully automated. Steps of the QIA and 3CB methods were lesion segmentation, characterization, and subsequent classification for malignancy in leave-one-case-out cross-validation. Performance assessment included box plots, Bland-Altman plots, and Receiver Operating Characteristic (ROC) analysis.ResultsThe area under the ROC curve (AUC) for distinguishing between benign and malignant lesions (invasive and DCIS) was 0.81 (standard error 0.07) for the "QIA alone" method, 0.72 (0.07) for "3CB alone" method, and 0.86 (0.04) for "QIA+3CB" combined. The difference in AUC was 0.043 between "QIA + 3CB" and "QIA alone" but failed to reach statistical significance (95% confidence interval [-0.17 to + 0.26]).ConclusionsIn this pilot study analyzing the new 3CB imaging modality, knowledge of the composition of breast lesions and their periphery appeared additive in combination with existing mammographic QIA methods for the distinction between different benign and malignant lesion types.

PurposeHigh spectral and spatial resolution magnetic resonance imaging (HiSS MRI) yields information on the local environment of suspicious lesions. Previous work has demonstrated the advantages of HiSS (complete fat-suppression, improved image contrast, no required contrast agent, etc.), leading to initial investigations of water resonance lineshape for the purpose of breast lesion classification. The purpose of this study is to investigate a quantitative imaging biomarker, which characterizes non-Lorentzian components of the water resonance in HiSS MRI datasets, for computer-aided diagnosis (CADx).MethodsThe inhomogeneous broadening and non-Lorentzian or "off-peak" components seen in the water resonance of proton spectra of breast HiSS images are analyzed by subtracting a Lorentzian fit from the water peak spectra and evaluating the difference spectrum or "residual." The maxima of these residuals (referred to hereafter as "off-peak components") tend to be larger in magnitude in malignant lesions, indicating increased broadening in malignant lesions. The authors considered only those voxels with the highest magnitude off-peak components in each lesion, with the number of selected voxels dependent on lesion size. Our voxel-based method compared the magnitudes and frequencies of off-peak components of all voxels from all lesions in a database that included 15 malignant and 8 benign lesions (yielding ≈ 3900 voxels) based on the lesions' biopsy-confirmed diagnosis. Lesion classification was accomplished by comparing the average off-peak component magnitudes and frequencies in malignant and benign lesions. The area under the ROC curve (AUC) was used as a figure of merit for both the voxel-based and lesion-based methods.ResultsIn the voxel-based task of distinguishing voxels from malignant and benign lesions, off-peak magnitude yielded an AUC of 0.88 (95% confidence interval [0.84, 0.91]). In the lesion-based task of distinguishing malignant and benign lesions, average off-peak magnitude yielded an AUC 0.83 (95% confidence interval [0.61, 0.98]).ConclusionsThese promising AUC values suggest that analysis of the water-resonance in each HiSS image voxel using "residual analysis" could have high diagnostic utility and could be used to enhance current CADx methods and allow detection of breast cancer without the need to inject contrast agents.