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@article{1542776,
author = {Kotrbová, Anna and Štěpka, Karel and Maška, Martin and Pálenik, Juraj and Ilkovics, Ladislav and Klemová, Dobromila and Kravec, Marek and Hubatka, František and Dave, Zankruti and Hampl, Aleš and Bryja, Vítězslav and Matula, Pavel and Pospíchalová, Vendula},
article_number = {1},
doi = {http://dx.doi.org/10.1080/20013078.2018.1560808},
keywords = {Exosome; cryo-electron microscopy; extracellular vesicles; image analysis; morphological seeded watershed; negative staining; segmentation; semi-automatic detection; size distribution profile; transmission electron microscopy},
language = {eng},
issn = {2001-3078},
journal = {Journal of Extracellular Vesicles},
title = {TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/},
volume = {8},
year = {2019}
}
TY - JOUR
ID - 1542776
AU - Kotrbová, Anna - Štěpka, Karel - Maška, Martin - Pálenik, Juraj - Ilkovics, Ladislav - Klemová, Dobromila - Kravec, Marek - Hubatka, František - Dave, Zankruti - Hampl, Aleš - Bryja, Vítězslav - Matula, Pavel - Pospíchalová, Vendula
PY - 2019
TI - TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images
JF - Journal of Extracellular Vesicles
VL - 8
IS - 1
SP - 1-13
EP - 1-13
PB - Taylor and Francis Ltd.
SN - 20013078
KW - Exosome
KW - cryo-electron microscopy
KW - extracellular vesicles
KW - image analysis
KW - morphological seeded watershed
KW - negative staining
KW - segmentation
KW - semi-automatic detection
KW - size distribution profile
KW - transmission electron microscopy
UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/
L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346710/
N2 - Extracellular vesicles (EVs) function as important conveyers of information between cells and thus can be exploited as drug delivery systems or disease biomarkers. Transmission electron microscopy (TEM) remains the gold standard method for visualisation of EVs, however the analysis of individual EVs in TEM images is time-consuming if performed manually. Therefore, we present here a software tool for computer-assisted evaluation of EVs in TEM images. TEM ExosomeAnalyzer detects EVs based on their shape and edge contrast criteria and subsequently analyses their size and roundness. The software tool is compatible with common negative staining protocols and isolation methods used in the field of EV research; even with challenging TEM images (EVs both lighter and darker than the background, images containing artefacts or precipitated stain, etc.). If the fully-automatic analysis fails to produce correct results, users can promptly adjust the detected seeds of EVs as well as their boundaries manually. The performance of our tool was evaluated for three different modes with variable levels of human interaction, using two datasets with various heterogeneity. The semi-automatic mode analyses EVs with high success rate in the homogenous dataset (F1 score 0.9094, Jaccard coefficient 0.8218) as well as in the highly heterogeneous dataset containing EVs isolated from cell culture medium and patient samples (F1 score 0.7619, Jaccard coefficient 0.7553). Moreover, the extracted size distribution profiles of EVs isolated from malignant ascites of ovarian cancer patients overlap with those derived by cryo-EM and are comparable to NTA- and TRPS-derived data. In summary, TEM ExosomeAnalyzer is an easy-to-use software tool for evaluation of many types of vesicular microparticles and is available at http://cbia.fi.muni.cz/exosome-analyzer free of charge for non-commercial and research purposes. The web page contains also detailed description how to use the software tool including a video tutorial.
ER -
KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA and Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. \textit{Journal of Extracellular Vesicles}. Taylor and Francis Ltd., 2019, vol.~8, No~1, p.~1-13. ISSN~2001-3078. Available from: https://dx.doi.org/10.1080/20013078.2018.1560808.
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