This article explains how CellProfiler™ can be used to automatically analyze kidney histology photomicrographs from samples stained with Masson’s trichrome stain to assess the percentage of fibrosis in an experimental animal model of CKD. CellProfiler™ is a program designed to analyze data obtained from biological samples and can process multiple images through pipelines, and the results can be exported to databases. Different programs are used to calculate the percentage of fibrosis however, the analysis is time-consuming since one image must be performed at a time. Most primary research on this disease requires evaluating the fibrosis index in animal model kidneys, specifically using Masson’s trichrome stain. With the help of this approach, researchers can make more studies faster and easier and find new antifibrogenic therapies to address the common and worldwide health problem caused by chronic kidney disease.Ĭhronic kidney disease (CKD) is a common and worldwide health problem and one of the most important causes of morbidity and mortality.
#Cellprofiler metadata software
The percentage of fibrosis using CellProfiler™ is similar to that obtained with the most widely used software for this kind of analysis called ImageJ. Here, we explain a method to conduct the same analysis but in a faster automated way with the assistance of a computer and a software package called CellProfiler™. However, this analysis is time-consuming because it needs to be made one image at a time and there are hundreds of samples in an animal model study. Some researchers use programs to make the evaluation of fibrosis easier. In these studies, it is essential to evaluate the percentage of fibrosis (growth of fibrotic tissue similar to a scar in response to damage) to know the degree of kidney damage. Researchers use animals as models to replicate the human body’s behavior to understand this disease. Thus, they cannot filter blood effectively and cause waste accumulation in the organism, leading to serious health problems. analysis/cpinp: containing the acquisition_metadata.csv, full_channelmeta.csv, and probab_channelmeta_manual.Chronic kidney disease is a health problem in which the kidneys cannot function normally.analysis/cpout/panel.csv: the panel file was copied into the final output folder.
#Cellprofiler metadata full
The analysis/cpout/images folder contains following files: txt files in the following folder structure: ├── _s0_a1_ac_ilastik.tiff The Hyperion Imaging System produces vendor controlled. To get started, please refer to the instructions here. Please follow the preprocessing.ipynb script to pre-process the raw data. During the first step of the segmentation pipeline, raw data need to be converted to file formats that can be read-in by external software ( Fiji, R, python, histoCAT).
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