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Related Experiment Video

Updated: Sep 26, 2025

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Published on: May 3, 2013

Autophagy profiling in single cells with open source CellProfiler-based image analysis.

David S Schüssele¹, Patricia K Haller^1,2, Maximilian L Haas¹

¹Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany.

|April 18, 2022

Summary

This summary is machine-generated.

This study introduces an automated CellProfiler method for quantifying autophagy using fluorescent protein imaging. This approach enables rapid and reliable single-cell analysis of autophagy markers like WIPI1.

Keywords:

Airyscan microscopy CellProfiler SQSTM1/p62 WIPI1 autophagy lipid droplets

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Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

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Published on: May 3, 2013

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Ferritinophagy: Assessing the Selective Degradation of Iron by Autophagy in Human Fibroblasts

Ferritinophagy: Assessing the Selective Degradation of Iron by Autophagy in Human Fibroblasts

Published on: February 23, 2024

Area of Science:

Cell Biology
Microscopy
Bioinformatics

Background:

Single-cell autophagy analysis commonly uses fluorescence microscopy to quantify autophagic puncta.
Manual counting of these puncta is time-consuming and less reliable than automated methods.
Automated analysis offers improved speed and accuracy for autophagy research.

Purpose of the Study:

To develop and present an open-source CellProfiler software pipeline for automated, quantitative analysis of macroautophagy/autophagy.
To provide detailed protocols and ready-to-use pipelines for assessing autophagy markers like GFP-tagged WIPI1.
To enable adaptable and high-throughput analysis of selective autophagy forms.

Main Methods:

Utilized CellProfiler software for image analysis of autophagy-related proteins.
Employed fluorescence microscopy (Airyscan, confocal laser-scanning) to acquire images of GFP-tagged WIPI1.
Developed specific pipelines for WIPI1, endogenous SQSTM1/p62, and lipid droplet analysis.

Main Results:

Presented a validated CellProfiler protocol for quantitative autophagy assessment.
Demonstrated the adaptability of the pipelines for different autophagy markers and cell types.
Showcased the potential for high-throughput screening of autophagy processes.

Conclusions:

The developed CellProfiler method provides a reliable and efficient tool for single-cell autophagy quantification.
This open-source approach facilitates broader adoption and adaptation in autophagy research.
The protocol supports various autophagy markers and can be applied to high-throughput studies.