geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis


, : AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis. Frontiers in Neuroinformatics 10: 37-37

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 MATLAB-based 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. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.

US$19.90

PMID: 27594833

DOI: 10.3389/fninf.2016.00037


Other references

Culmsee, C.; Kruman, I.I.; Yu, Q.; Zhu, X.; Camandola, S.; Chan, S.L.; Guo, Z.; Junker, V.; Krieglstein, J.; Greig, N.; Mattson, M.P., 2001: Evidence for the emerging role of DNA-damage and activation of p53 in neuron cell death. Naunyn-Schmiedeberg's Archives of Pharmacology 363(4 Supplement): R91

Shubber, A.H.; Doxey, D.L.; Black, W.J.; FitzSimons, J., 1979: Immunoglobulin levels in ewe colostrum and in lamb serum. The immunoglobulin content of ewe colostrum falls rapidly after the first suckling and reaches a low level 36 h after the first feed. The whey content of colostrum will rise by more than 50 per cent during the same period. The production of colost...

Boer, L.L.; Naue, J.; de Rooy, L.; Oostra, R-Jan., 2017: Detection of G1138A Mutation of the FGFR3 Gene in Tooth Material from a 180-Year-Old Museological Achondroplastic Skeleton. Throughout the last four centuries, many anatomical museums across the world have collected teratological specimens that became precious objects. These can be regarded as spirits of the past which have captured the morphology of diseases through t...

Bornstein, R.F., 2007: On integrating variables and separating facts in the complex relationship between dependency and domestic violence. American Psychologist 62(7): 709-711

Das, T.; Das, S.; Chakraborty, S., 2009: Influences of streaming potential on cross stream migration of flexible polymer molecules in nanochannel flows. We execute augmented Brownian dynamics (BD) simulation studies to show that the migration of flexible polyelectrolyte chains through nanochannels may be strongly governed by a complicated interplay between the electroviscous effects, near-wall int...

Griffin, J.F.; Larson, D.L.; Portoghese, P.S., 1986: Crystal structures of alpha- and beta-funaltrexamine: conformational requirement of the fumaramate moiety in the irreversible blockage of mu opioid receptors. alpha- and beta-funaltrexamine (alpha- and beta-FNA, 1a and 1b) are naltrexone derivatives differing only in chirality at C(6). Both epimers bind to mu opioid receptors in GPI and MVD preparations, but only the beta-epimer irreversibly blocks thes...

Holsti L.R.; Salmo M.; Elkind M.M., 1982: Unconventional fractionation in the treatment of primary and secondary lung tumors. Kaercher, K H , H D Kogelnik And G Reinartz (Ed ) Progress in Radio-Oncology; 2nd International Meeting, Baden, Austria, 1981 Xxiv+485p Raven Press: New York, N Y , Usa Illus P325-330

Otto, G.F.; Skriabin, K.I., 1978: In memoriam. Centenary of academician K. I. Skrjabin. Journal of Parasitology 64(6): 1119-1119

Wobeser, G.; Galmut, E.A., 1984: Rate of digestion of blowfly maggots by ducks. Journal of Wildlife Diseases 20(2): 154-155

Bios-Choussy, M.B.rbier, M., 1977: Structure of sarpedobilin, a butterfly bile pigment. Experientia 33 (11) 1407-1410