MitoSegNet: Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology.

Kritarth Singh,Christian A Fischer,Carsten Marr,Laura Besora-Casals,Stéphane G Rolland,Michael Duchen,Barbara Conradt,Simon Haeussler

doi:10.1016/j.isci.2020.101601

Abstract

SummaryWhile the analysis of mitochondrial morphology has emerged as a key tool in the study of mitochondrial function, efficient quantification of mitochondrial microscopy images presents a challenging task and bottleneck for statistically robust conclusions. Here, we present Mitochondrial Segmentation Network (MitoSegNet), a pretrained deep learning segmentation model that enables researchers to easily exploit the power of deep learning for the quantification of mitochondrial morphology. We tested the performance of MitoSegNet against three feature-based segmentation algorithms and the machine-learning segmentation tool Ilastik. MitoSegNet outperformed all other methods in both pixelwise and morphological segmentation accuracy. We successfully applied MitoSegNet to unseen fluorescence microscopy images of mitoGFP expressing mitochondria in wild-type and catp-6ATP13A2 mutant C. elegans adults. Additionally, MitoSegNet was capable of accurately segmenting mitochondria in HeLa cells treated with fragmentation inducing reagents. We provide MitoSegNet in a toolbox for Windows and Linux operating systems that combines segmentation with morphological analysis.

Highlights

Cellular organelles are integral to eukaryotic cells and their functions
We show that MitoSegNet can be successfully used to analyze mitochondrial morphology in HeLa cells
We present MitoSegNet, a segmentation model that exploits the power of deep learning to address the challenging problem of accurate mitochondria segmentation

Summary

SUMMARY

While the analysis of mitochondrial morphology has emerged as a key tool in the study of mitochondrial function, efficient quantification of mitochondrial microscopy images presents a challenging task and bottleneck for statistically robust conclusions. We present Mitochondrial Segmentation Network (MitoSegNet), a pretrained deep learning segmentation model that enables researchers to exploit the power of deep learning for the quantification of mitochondrial morphology. We tested the performance of MitoSegNet against three featurebased segmentation algorithms and the machine-learning segmentation tool Ilastik. MitoSegNet outperformed all other methods in both pixelwise and morphological segmentation accuracy. We successfully applied MitoSegNet to unseen fluorescence microscopy images of mitoGFP expressing mitochondria in wild-type and catp-6ATP13A2 mutant C. elegans adults. We provide MitoSegNet in a toolbox for Windows and Linux operating systems that combines segmentation with morphological analysis

INTRODUCTION

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Transparent Methods