Skip to main content

Main menu

  • Home
  • Content
    • Published Ahead of Print
    • Current Issue
    • JASN Podcasts
    • Article Collections
    • Archives
    • Kidney Week Abstracts
    • Saved Searches
  • Authors
    • Submit a Manuscript
    • Author Resources
  • Editorial Team
  • Editorial Fellowship
    • Editorial Fellowship Team
    • Editorial Fellowship Application Process
  • More
    • About JASN
    • Advertising
    • Alerts
    • Feedback
    • Impact Factor
    • Reprints
    • Subscriptions
  • ASN Kidney News
  • Other
    • ASN Publications
    • CJASN
    • Kidney360
    • Kidney News Online
    • American Society of Nephrology

User menu

  • Subscribe
  • My alerts
  • Log in
  • My Cart

Search

  • Advanced search
American Society of Nephrology
  • Other
    • ASN Publications
    • CJASN
    • Kidney360
    • Kidney News Online
    • American Society of Nephrology
  • Subscribe
  • My alerts
  • Log in
  • My Cart
Advertisement
American Society of Nephrology

Advanced Search

  • Home
  • Content
    • Published Ahead of Print
    • Current Issue
    • JASN Podcasts
    • Article Collections
    • Archives
    • Kidney Week Abstracts
    • Saved Searches
  • Authors
    • Submit a Manuscript
    • Author Resources
  • Editorial Team
  • Editorial Fellowship
    • Editorial Fellowship Team
    • Editorial Fellowship Application Process
  • More
    • About JASN
    • Advertising
    • Alerts
    • Feedback
    • Impact Factor
    • Reprints
    • Subscriptions
  • ASN Kidney News
  • Follow JASN on Twitter
  • Visit ASN on Facebook
  • Follow JASN on RSS
  • Community Forum
Basic Research
You have accessRestricted Access

PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images

Darshana Govind, Jan U. Becker, Jeffrey Miecznikowski, Avi Z. Rosenberg, Julien Dang, Pierre Louis Tharaux, Rabi Yacoub, Friedrich Thaiss, Peter F. Hoyer, David Manthey, Brendon Lutnick, Amber M. Worral, Imtiaz Mohammad, Vighnesh Walavalkar, John E. Tomaszewski, Kuang-Yu Jen and Pinaki Sarder
JASN November 2021, 32 (11) 2795-2813; DOI: https://doi.org/10.1681/ASN.2021050630
Darshana Govind
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jan U. Becker
2Institute of Pathology, University Hospital of Cologne, Cologne, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey Miecznikowski
3Department of Biostatistics, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Avi Z. Rosenberg
4Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Avi Z. Rosenberg
Julien Dang
5Paris Cardiovascular Center, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pierre Louis Tharaux
5Paris Cardiovascular Center, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Pierre Louis Tharaux
Rabi Yacoub
6Department of Internal Medicine, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Friedrich Thaiss
7Third Medical Department of Clinical Medicine, University Hospital Hamburg Eppendorf, Hamburg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter F. Hoyer
8Pediatric Nephrology, University Hospital Essen, Essen, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Manthey
9Kitware Incorporated, Clifton Park, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brendon Lutnick
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Brendon Lutnick
Amber M. Worral
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Imtiaz Mohammad
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vighnesh Walavalkar
10Department of Pathology, University of California San Francisco, San Francisco, California
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John E. Tomaszewski
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kuang-Yu Jen
11Department of Pathology and Laboratory Medicine, University of California, Sacramento, California
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kuang-Yu Jen
Pinaki Sarder
1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Article
  • Figures & Data Supps
  • Info & Metrics
  • View PDF
Loading

Visual Abstract

Figure
  • Download figure
  • Open in new tab
  • Download powerpoint

Significance Statement

Podocytes are depleted in several renal parenchymal processes. The current gold standard to identify podocytes considers histopathologic staining of nuclei using specific antibodies and manual enumeration, which is expensive and laborious. We have developed PodoSighter, a cloud-based tool for automated, label-free podocyte detection, and three-dimensional quantification from periodic acid–Schiff-stained histologic sections. A diverse dataset from rodent models of glomerular diseases (diabetic kidney disease, crescentic GN, and dose-dependent direct podocyte toxicity and depletion), human biopsies for steroid resistant nephrotic syndrome, and human autopsy tissue, demonstrate generalizability of the tool. Samples were derived from multiple laboratory, supporting broad application. This tool may facilitate clinical assessment and research involving podocyte morphometry.

Abstract

Background Podocyte depletion precedes progressive glomerular damage in several kidney diseases. However, the current standard of visual detection and quantification of podocyte nuclei from brightfield microscopy images is laborious and imprecise.

Methods We have developed PodoSighter, an online cloud-based tool, to automatically identify and quantify podocyte nuclei from giga-pixel brightfield whole-slide images (WSIs) using deep learning. Ground-truth to train the tool used immunohistochemically or immunofluorescence-labeled images from a multi-institutional cohort of 122 histologic sections from mouse, rat, and human kidneys. To demonstrate the generalizability of our tool in investigating podocyte loss in clinically relevant samples, we tested it in rodent models of glomerular diseases, including diabetic kidney disease, crescentic GN, and dose-dependent direct podocyte toxicity and depletion, and in human biopsies from steroid-resistant nephrotic syndrome and from human autopsy tissues.

Results The optimal model yielded high sensitivity/specificity of 0.80/0.80, 0.81/0.86, and 0.80/0.91, in mouse, rat, and human images, respectively, from periodic acid–Schiff-stained WSIs. Furthermore, the podocyte nuclear morphometrics extracted using PodoSighter were informative in identifying diseased glomeruli. We have made PodoSighter freely available to the general public as turnkey plugins in a cloud-based web application for end users.

Conclusions Our study demonstrates an automated computational approach to detect and quantify podocyte nuclei in standard histologically stained WSIs, facilitating podocyte research, and enabling possible future clinical applications.

  • podocyte detection
  • deep learning
  • pix2pix GAN
  • Deeplab
  • cloud
  • cloud computing
  • urinary tract
  • viscera
  • podocytes
  • CNN
  • Copyright © 2021 by the American Society of Nephrology
View Full Text

If you are:

  • an ASN member, select the "ASN Member" login button. 
  • an individual subscriber, login with you User Name and Password.
  • an Institutional user, select the Institution option where you will be presented with a list of Shibboleth federations. If you do not see your federation, contact publications@asn-online.org. 

ASN MEMBER LOGIN

ASN MEMBER LOGIN

Log in using your username and password

Forgot your user name or password?

Log in through your institution

You may be able to gain access using your login credentials for your institution. Contact your library if you do not have a username and password.

Purchase access

Pay Per Article - You may access this article (from the computer you are currently using) for 1 day for US$34.00

In order to get access to the article, you must have an account.  If you have an account, enter your user name and password into the boxes above. If you do not have an account, follow the instructions below to create one.  Once you have purchased the article, you will have access to it for 24 hours.  

Steps for Creating an Account:

Click the "Purchase Access" button.  The page will redisplay with the following message at the top of the screen. In the message, click to create an account. 

When you create the account, you will be asked to register a user name, email address and you will need to create a password that is at least eight characters in length.  You do not need an ASN Member number to complete the form. As you move through the registration page, you will have to verify you are a person by completing a Captcha request.   Lastly, your first and last name will be required. 

Once your information is successfully saved, the system will redisplay the home page of the journal.  From there, navigate back to the article to purchase.  Select the article and at the bottom of the page, use the credentials you just created to login. The article will be added to your shopping cart.  You can continue to navigate across JASN and CJASN adding to your cart from both journals. When you are ready to complete your purchse, select the Shopping Cart from the upper right hand corner of the page and follow the onscreen instructions. 

PreviousNext
Back to top

In this issue

Journal of the American Society of Nephrology: 32 (11)
Journal of the American Society of Nephrology
Vol. 32, Issue 11
November 2021
  • Table of Contents
  • Table of Contents (PDF)
  • About the Cover
  • Index by author
View Selected Citations (0)
Print
Download PDF
Sign up for Alerts
Email Article
Thank you for your help in sharing the high-quality science in JASN.
Enter multiple addresses on separate lines or separate them with commas.
PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images
(Your Name) has sent you a message from American Society of Nephrology
(Your Name) thought you would like to see the American Society of Nephrology web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images
Darshana Govind, Jan U. Becker, Jeffrey Miecznikowski, Avi Z. Rosenberg, Julien Dang, Pierre Louis Tharaux, Rabi Yacoub, Friedrich Thaiss, Peter F. Hoyer, David Manthey, Brendon Lutnick, Amber M. Worral, Imtiaz Mohammad, Vighnesh Walavalkar, John E. Tomaszewski, Kuang-Yu Jen, Pinaki Sarder
JASN Nov 2021, 32 (11) 2795-2813; DOI: 10.1681/ASN.2021050630

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images
Darshana Govind, Jan U. Becker, Jeffrey Miecznikowski, Avi Z. Rosenberg, Julien Dang, Pierre Louis Tharaux, Rabi Yacoub, Friedrich Thaiss, Peter F. Hoyer, David Manthey, Brendon Lutnick, Amber M. Worral, Imtiaz Mohammad, Vighnesh Walavalkar, John E. Tomaszewski, Kuang-Yu Jen, Pinaki Sarder
JASN Nov 2021, 32 (11) 2795-2813; DOI: 10.1681/ASN.2021050630
del.icio.us logo Digg logo Reddit logo Twitter logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like

Jump to section

  • Article
    • Visual Abstract
    • Abstract
    • Methods
    • Results
    • Discussion
    • Disclosures
    • Funding
    • Acknowledgments
    • Data Availability Statement
    • Code Availability
    • Supplemental Material
    • Footnotes
    • References
  • Figures & Data Supps
  • Info & Metrics
  • View PDF

More in this TOC Section

  • Single-Cell Chromatin and Gene-Regulatory Dynamics of Mouse Nephron Progenitors
  • Myeloid CCR2 Promotes Atherosclerosis after AKI
  • Intestinal Bacterial Translocation Contributes to Diabetic Kidney Disease
Show more Basic Research

Cited By...

  • No citing articles found.
  • Google Scholar

Similar Articles

Related Articles

  • PubMed
  • Google Scholar

Keywords

  • podocyte detection
  • deep learning
  • pix2pix GAN
  • Deeplab
  • cloud
  • cloud computing
  • urinary tract
  • viscera
  • podocytes
  • CNN

Articles

  • Current Issue
  • Early Access
  • Subject Collections
  • Article Archive
  • ASN Annual Meeting Abstracts

Information for Authors

  • Submit a Manuscript
  • Author Resources
  • Editorial Fellowship Program
  • ASN Journal Policies
  • Reuse/Reprint Policy

About

  • JASN
  • ASN
  • ASN Journals
  • ASN Kidney News

Journal Information

  • About JASN
  • JASN Email Alerts
  • JASN Key Impact Information
  • JASN Podcasts
  • JASN RSS Feeds
  • Editorial Board

More Information

  • Advertise
  • ASN Podcasts
  • ASN Publications
  • Become an ASN Member
  • Feedback
  • Follow on Twitter
  • Password/Email Address Changes
  • Subscribe to ASN Journals
  • Wolters Kluwer Partnership

© 2022 American Society of Nephrology

Print ISSN - 1046-6673 Online ISSN - 1533-3450

Powered by HighWire