AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Scientific Reports
Aldo ZaimiJulien Cohen-Adad

Abstract

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only a few methods are publicly available. We introduce AxonDeepSeg, an open-source software that performs axon and myelin segmentation of microscopic images using deep learning. AxonDeepSeg features: (i) a convolutional neural network architecture; (ii) an easy training procedure to generate new models based on manually-labelled data and (iii) two ready-to-use models trained from scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Results show high pixel-wise accuracy across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and 84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed and morphological me...Continue Reading

References

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Jan 10, 2018·Frontiers in Neuroanatomy·Ariane SalianiJulien Cohen-Adad

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Citations

Nov 30, 2018·Journal of the Peripheral Nervous System : JPNS·Daniel MoiseevJun Li
Sep 6, 2019·Scientific Reports·Graham RobertsYuanyuan Zhu
Apr 17, 2019·Scientific Reports·Ali AbdollahzadehAlejandra Sierra
Jan 8, 2019·International Journal of Computer Assisted Radiology and Surgery·Marco VidottoSara Moccia
May 18, 2020·Scientific Reports·Matthew D RitchC Ross Ethier
Oct 1, 2020·Computational and Structural Biotechnology Journal·Erik Meijering
Nov 2, 2020·Journal of Neuroscience Methods·Siawoosh Mohammadi, Martina F Callaghan
Jan 11, 2021·Medical Image Analysis·Thomas YuJean-Philippe Thiran
Sep 16, 2020·Journal of Neuroscience Methods·Sibel Çimen YetişB Uğur Töreyin
Sep 5, 2021·Proceedings of the National Academy of Sciences of the United States of America·Marco VidottoDaniele Dini
Dec 22, 2021·Translational Vision Science & Technology·Wenxiang DengMona K Garvin

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Methods Mentioned

BETA
electron microscopy
light microscopy
scanning
transmission electron microscopy
scanning electron microscopy
optical microscopy

Software Mentioned

TensorFlow
AxonDeepSeg
AxonSeg
Jupyter

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