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Warner, Joshua D

Mayo Clinic

Department of Biomedical Engineering, Mayo Clinic , Rochester, MN , USA.

Citations 3

Automatic total kidney volume measurement on follow-up magnetic resonance images to facilitate monitoring of autosomal dominant polycystic kidney disease progression
Kline, Timothy L. , Korfiatis, Panagiotis , Edwards, Marie E., Warner, Joshua , Irazabal, María V. , King, Bernard F., Torres, Vicente E. , Warner, Joshua D, Erickson, Bradley J. , Torres, Vicente E , Irazabal, Maria V

Nephrology Dialysis Transplantation | September 11, 2015 | Volume: 31 | Issue: 2 | Pages: 241-248

10.1093/ndt/gfv314 Get It

Abstract Background Renal imaging examinations provide high-resolution information about the anatomic structure of the kidneys and are used to measure total kidney volume (TKV) in autosomal dominant polycystic kidney disease (ADPKD) patients. TKV has become the gold-standard image biomarker for ADPKD progression at early stages of the disease and is used in clinical trials to characterize treatment efficacy. Automated methods to segment the kidneys and measure TKV are desirable because of the long time requirement for manual approaches such as stereology or planimetry tracings. However, ADPKD kidney segmentation is complicated by a number of factors, including irregular kidney shapes and variable tissue signal at the kidney borders. Methods We describe an image processing approach that overcomes these problems by using a baseline segmentation initialization to provide automatic segmentation of follow-up scans obtained years apart. We validated our approach using 20 patients with complete baseline and follow-up T1-weighted magnetic resonance images. Both manual tracing and stereology were used to calculate TKV, with two observers performing manual tracings and one observer performing repeat tracings. Linear correlation and Bland–Altman analysis were performed to compare the different approaches. Results Our automated approach measured TKV at a level of accuracy (mean difference ± standard error = 0.99 ± 0.79%) on par with both intraobserver (0.77 ± 0.46%) and interobserver variability (1.34 ± 0.70%) of manual tracings. All approaches had excellent agreement and compared favorably with ground-truth manual tracing with interobserver, stereological and automated approaches having 95% confidence intervals ∼±100 mL. Conclusions Our method enables fast, cost-effective and reproducible quantification of ADPKD progression that will facilitate and lower the costs of clinical trials in ADPKD and other disorders requiring accurate, longitudinal kidney quantification. In addition, it will hasten the routine use of TKV as a prognostic biomarker in ADPKD.
Utilizing magnetization transfer imaging to investigate tissue remodeling in a murine model of autosomal dominant polycystic kidney disease
Kline, Timothy L. , Irazabal, María V. , Ebrahimi, Behzad , Udoji, Kelly N., Warner, Joshua , Korfiatis, Panagiotis , Mishra, Prasanna K. , Venkatesh, Sudhakar K. , Lerman, Lilach O. , Harris, Peter C. , Torres, Vicente E. , King, Bernard F., Hopp, Katharina , Warner, Joshua D, Macura, Slobodan I, Macura, Slobodan , Erickson, Bradley J. , Harris, Peter C , Torres, Vicente E , Venkatesh, Sudhakar K , Irazabal, Maria V

Magnetic Resonance in Medicine | May 14, 2015 | Volume: 75 | Issue: 4 | Pages: 1466-1473

10.1002/mrm.25701 Get It

PurposeNoninvasive imaging techniques that quantify renal tissue composition are needed to more accurately ascertain prognosis and monitor disease progression in polycystic kidney disease (PKD). Given the success of magnetization transfer (MT) imaging to characterize various tissue remodeling pathologies, it was tested on a murine model of autosomal dominant PKD.MethodsC57Bl/6 Pkd1 R3277C mice at 9, 12, and 15 months were imaged with a 16.4T MR imaging system. Images were acquired without and with RF saturation in order to calculate MT ratio (MTR) maps. Following imaging, the mice were euthanized and kidney sections were analyzed for cystic and fibrotic indices, which were compared with statistical parameters of the MTR maps.ResultsThe MTR‐derived mean, median, 25th percentile, skewness, and kurtosis were all closely related to indices of renal pathology, including kidney weight/body weight, cystic index, and percent of remaining parenchyma. The correlation between MTR and histology‐derived cystic and fibrotic changes was R2 = 0.84 and R2 = 0.70, respectively.ConclusionMT imaging provides a new, noninvasive means of measuring tissue remodeling PKD changes and may be better suited for characterizing renal impairment compared with conventional MR techniques. Magn Reson Med 75:1466–1473, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance.
scikit-image: image processing in Python
Schönberger, Johannes L., Nunez-Iglesias, Juan , Boulogne, François , Warner, Joshua , Yager, Neil , Gouillart, Emmanuelle , Warner, Joshua D, Walt, Stéfan van der , Yu, Tony

PeerJ | June 19, 2014 | Volume: 2 | Issue: No issue available | Pages: e453

10.7717/peerj.453 Get It