Development of a multiple convolutional neural network-facilitated diagnostic screening program for immunofluorescence images of IgA nephropathy and idiopathic membranous nephropathy

Peng Xia; Zhilong Lv; Yubing Wen; Baichuan Zhang; Xuesong Zhao; Boyao Zhang; Ying Wang; Haoyuan Cui; Chuanpeng Wang; Hua Zheng; Yan Qin; Lijun Sun; Nan Ye; Hong Cheng; Li Yao; Hua Zhou; Junhui Zhen; Zhao Hu; Weiguo Zhu; Fa Zhang; Xuemei Li; Fei Ren; Limeng Chen

doi:10.1093/ckj/sfad153

Development of a multiple convolutional neural network-facilitated diagnostic screening program for immunofluorescence images of IgA nephropathy and idiopathic membranous nephropathy

Clin Kidney J. 2023 Jul 18;16(12):2503-2513. doi: 10.1093/ckj/sfad153. eCollection 2023 Dec.

Authors

Peng Xia¹, Zhilong Lv^{2

3}, Yubing Wen¹, Baichuan Zhang⁴, Xuesong Zhao¹, Boyao Zhang⁴, Ying Wang¹, Haoyuan Cui¹, Chuanpeng Wang¹, Hua Zheng¹, Yan Qin¹, Lijun Sun⁵, Nan Ye⁵, Hong Cheng⁵, Li Yao⁶, Hua Zhou⁷, Junhui Zhen⁸, Zhao Hu⁹, Weiguo Zhu¹⁰, Fa Zhang², Xuemei Li¹, Fei Ren², Limeng Chen¹

Affiliations

¹ Department of Nephrology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
² Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
³ School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing, China.
⁴ Beijing Zhijian Life Technology, Beijing, China.
⁵ Department of Nephrology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
⁶ Department of Nephrology, First Hospital Affiliated to China Medical University, Shenyang, China.
⁷ Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China.
⁸ Department of Pathology, Qilu Hospital of Shandong University, Jinan, China.
⁹ Department of Nephrology, Qilu Hospital of Shandong University, Jinan, China.
¹⁰ Department of Information, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Abstract

Background: Immunoglobulin A nephropathy (IgAN) and idiopathic membranous nephropathy (IMN) are the most common glomerular diseases. Immunofluorescence (IF) tests of renal tissues are crucial for the diagnosis. We developed a multiple convolutional neural network (CNN)-facilitated diagnostic program to assist the IF diagnosis of IgAN and IMN.

Methods: The diagnostic program consisted of four parts: a CNN trained as a glomeruli detection module, an IF intensity comparator, dual-CNN (D-CNN) trained as a deposition appearance and location classifier and a post-processing module. A total of 1573 glomerular IF images from 1009 patients with glomerular diseases were used for the training and validation of the diagnostic program. A total of 1610 images of 426 patients from different hospitals were used as test datasets. The performance of the diagnostic program was compared with nephropathologists.

Results: In >90% of the tested images, the glomerulus location module achieved an intersection over union >0.8. The accuracy of the D-CNN in recognizing irregular granular mesangial deposition and fine granular deposition along the glomerular basement membrane was 96.1% and 93.3%, respectively. As for the diagnostic program, the accuracy, sensitivity and specificity of diagnosing suspected IgAN were 97.6%, 94.4% and 96.0%, respectively. The accuracy, sensitivity and specificity of diagnosing suspected IMN were 91.7%, 88.9% and 95.8%, respectively. The corresponding areas under the curve (AUCs) were 0.983 and 0.935. When tested with images from the outside hospital, the diagnostic program showed stable performance. The AUCs for diagnosing suspected IgAN and IMN were 0.972 and 0.948, respectively. Compared with inexperienced nephropathologists, the program showed better performance.

Conclusion: The proposed diagnostic program could assist the IF diagnosis of IgAN and IMN.

Keywords: IgA nephropathy; convolutional neural network; idiopathic membranous nephropathy; immunofluorescence.