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AxonSeg: open source software for axon and myelin segmentation and morphometric analysis

Aldo Zaimi, Tanguy Duval, Alicja Gasecka, Daniel Côté, Nikola Stikov and Julien Cohen-Adad

Article (2016)

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Cite this document: Zaimi, A., Duval, T., Gasecka, A., Côté, D., Stikov, N. & Cohen-Adad, J. (2016). AxonSeg: open source software for axon and myelin segmentation and morphometric analysis. Frontiers in Neuroinformatics, 10, p. 1-13. doi:10.3389/fninf.2016.00037
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Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy (SEM) only). Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLABbased graphical user interface (GUI) and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i) image pre-processing; (ii) pre-segmentation of axons over a cropped image and discriminant analysis (DA) to select the best parameters based on axon shape and intensity information; (iii) automatic axon and myelin segmentation over the full image; and (iv) atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM), SEM and coherent anti-Stokes Raman scattering (CARS) microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology.

Uncontrolled Keywords

axon; discriminant analysis; g-ratio; graphical user interface; histology; microscopy; myelin; segmentation

Open Access document in PolyPublie
Subjects: 1900 Génie biomédical > 1900 Génie biomédical
2700 Technologie de l'information > 2705 Logiciels et développement
9000 Sciences de la santé > 9000 Sciences de la santé
Department: Institut de génie biomédical
Research Center: Non applicable
Funders: Canada Research Chair in Quantitative Magnetic Resonance Imaging, Canadian Institute of Health Research, Fonds de recherche du Québec--Santé, Fonds de recherche du Québec--Nature et technologies, CRSNG/NSERC
Grant number: 230815, CIHR FDN-143263, 28826, 2015-PR-182754, 435897-2013
Date Deposited: 07 Dec 2018 13:22
Last Modified: 08 Apr 2021 10:43
PolyPublie URL: https://publications.polymtl.ca/3501/
Document issued by the official publisher
Journal Title: Frontiers in Neuroinformatics (vol. 10)
Publisher: Frontiers
Official URL: https://doi.org/10.3389/fninf.2016.00037


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