Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Jan 24;9:521. doi: 10.1038/s41598-018-36741-1

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Segmentation of glomeruli from mouse kidney perfused with MHI148-PEI and cleared with ECi using simple image processing pipeline: background removal using median filter, segmentation using Otsu thresholding in combination with binary morphological filters and 2-class classifier to filter only bigger glomeruli (class 1). The partially visible glomeruli and background objects were designated class 2. (a) Raw 3D data from small section of left mouse kidney. The raw data with specific settings is shown in Supplementary figure S13. (b) Segmented 3D data showing glomeruli using different group of colors based on the volume histogram shown in (c). (c) Volume histogram showing six groups where red color represents the group with smallest. (d) Leica LAS X software to create custom made analysis pipeline as shown by a sequence on left. The left and right images depict raw and segmented data (only class 2).