TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images

References

• Yanez-Mo M, Siljander PR, Andreu Z, et al. Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015;4:27066. PubMed PMID: 25979354; PubMed Central PMCID: PMC4433489.
   PubMed Web of Science ®Google Scholar
• Steinbichler TB, Dudas J, Riechelmann H, et al. The role of exosomes in cancer metastasis. Semin Cancer Biol. 2017 Jun;44:170–13. PubMed PMID: 28215970.
   PubMed Web of Science ®Google Scholar
• Raposo G, Stoorvogel W. Extracellular vesicles: exosomes, microvesicles, and friends. J Cell Biol. 2013 Feb 18;200(4):373–383. . PubMed PMID: 23420871; PubMed Central PMCID: PMC3575529.
   PubMed Web of Science ®Google Scholar
• Mirzaei H, Sahebkar A, Jaafari MR, et al. Diagnostic and therapeutic potential of exosomes in cancer: the beginning of a new tale? J Cell Physiol. 2017 Dec;232(12):3251–3260. PubMed PMID: 27966794.
   PubMed Web of Science ®Google Scholar
• Pospichalova V, Svoboda J, Dave Z, et al. Simplified protocol for flow cytometry analysis of fluorescently labeled exosomes and microvesicles using dedicated flow cytometer. J Extracell Vesicles. 2015;4:25530. PubMed PMID: 25833224; PubMed Central PMCID: PMC4382613.
   PubMed Web of Science ®Google Scholar
• Traikia M, Warschawski DE, Recouvreur M, et al. Formation of unilamellar vesicles by repetitive freeze-thaw cycles: characterization by electron microscopy and 31P-nuclear magnetic resonance. Eur Biophys J. 2000;29(3):184–195. PubMed PMID: 10968210.
   Web of Science ®Google Scholar
• Maas SL, de Vrij J, van der Vlist EJ, et al. Possibilities and limitations of current technologies for quantification of biological extracellular vesicles and synthetic mimics. J Control Release. 2015 Feb 28;200:87–96. PubMed PMID: 25555362; PubMed Central PMCID: PMC4324667.
   PubMed Web of Science ®Google Scholar
• Maas SL, De Vrij J, Broekman ML. Quantification and size-profiling of extracellular vesicles using tunable resistive pulse sensing. J vis exp. 2014 Oct 19;(92):e51623. PubMed PMID: 25350417; PubMed Central PMCID: PMC4335984. Doi:10.3791/51623
   Web of Science ®Google Scholar
• Štěpka K, Maška M, Pálenik JJ. et al. Automatic detection and segmentation of exosomes in transmission electron microscopy. In: Hua G, Jégou H. editors. Computer vision – ECCV 2016 workshops. Amsterdam, The Netherlands: Springer International Publishing, 2016:318–325. October 8-10 and 15-16, 2016, Proceedings, Part I. Cham.
   Google Scholar
• Soille P. Morphological Image Analysis. Vol. 2. Heidelberg, Germany: Springer-Verlag Berlin Heidelberg; 2004.
   Google Scholar
• Dragovic RA, Gardiner C, Brooks AS, et al. Sizing and phenotyping of cellular vesicles using nanoparticle tracking analysis. Nanomed. 2011 Dec;7(6):780–788. PubMed PMID: 21601655; PubMed Central PMCID: PMC3280380.
   PubMed Web of Science ®Google Scholar
• Coumans FA, van der Pol E, Boing AN, et al. Reproducible extracellular vesicle size and concentration determination with tunable resistive pulse sensing. J Extracell Vesicles. 2014;3:25922. PubMed PMID: 25498889; PubMed Central PMCID: PMC4263901.
   PubMedGoogle Scholar
• Cizmar P, Yuana Y. Detection and characterization of extracellular vesicles by transmission and cryo-transmission electron microscopy. Methods Mol Biol. 2017;1660:221–232. PubMed PMID: 28828660.
   PubMedGoogle Scholar
• Scarff CA, Fuller MJG, Thompson RF, et al. Variations on negative stain electron microscopy methods: tools for tackling challenging systems. J vis exp. 2018 Feb 6; 132: PubMed PMID: 29443097; PubMed Central PMCID: PMC5912373. doi: 10.3791/57199.
   Web of Science ®Google Scholar
• van der Pol E, Coumans FA, Grootemaat AE, et al. Particle size distribution of exosomes and microvesicles by transmission electron microscopy, flow cytometry, nanoparticle tracking analysis, and resistive pulse sensing. J Thromb Haemost. 2014 May 13 PubMed PMID: 24818656. DOI:10.1111/jth.12602.
   Web of Science ®Google Scholar
• van Niel G, D’Angelo G, Raposo G. Shedding light on the cell biology of extracellular vesicles. Nat Rev Mol Cell Biol. 2018 Apr;19(4):213–228. . PubMed PMID: 29339798.
   PubMed Web of Science ®Google Scholar
• Seyedhosseini M, Ellisman MH, Tasdizen T. Segmentation of mitochondria in electron microscopy images using algebraic curves. Proc IEEE Int Symp Biomed Imaging. 2013;2013: 860–863. PubMed PMID: 25132915; eng.
   Google Scholar
• Sommer C, Straehle C, Köthe U, et al., editors. Ilastik: interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro; 2011 March 30, 2011-April 2; Chicago, IL, USA; 2011.
   Google Scholar
• Arganda-Carreras I, Kaynig V, Rueden C, et al. Trainable Weka segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics. 2017 Aug 1;33(15):2424–2426. PubMed PMID: 28369169.
   PubMed Web of Science ®Google Scholar
• Goodfellow I, Bengio. Y, Courville A. Deep Learning. Cambridge, MA: MIT Press; 2016.
   Google Scholar
• Thery C, Amigorena S, Raposo G. et al. Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr Protoc Cell Biol. Juan S Bonifacino [et al]. 2006 Apr; Chapter 3: Unit3 22. doi: 10.1002/0471143030.cb0322s30. PubMed PMID: 18228490
   PubMedGoogle Scholar
• Jensen OA, Prause JU, Laursen H. Shrinkage in preparatory steps for SEM. A study on rabbit corneal endothelium. Albrecht Von Graefes Arch Klin Exp Ophthalmol. 1981;215(4): 233–242. PubMed PMID: 6164307.
   Google Scholar
• Yuana Y, Koning RI, Kuil ME, et al. Cryo-electron microscopy of extracellular vesicles in fresh plasma. J Extracell Vesicles. 2013 Dec;31:2. PubMed PMID: 24455109; PubMed Central PMCID: PMC3895263.
   Google Scholar
• Thompson RF, Walker M, Siebert CA, et al. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods. 2016 May 1;100:3–15. PubMed PMID: 26931652; PubMed Central PMCID: PMC4854231.
   PubMed Web of Science ®Google Scholar
• Sodar BW, Kittel A, Paloczi K, et al. Low-density lipoprotein mimics blood plasma-derived exosomes and microvesicles during isolation and detection. Sci Rep. 2016 Apr 18;6:24316. PubMed PMID: 27087061; PubMed Central PMCID: PMC4834552.
   PubMed Web of Science ®Google Scholar
• Simonsen JB. What are we looking at? Extracellular vesicles, lipoproteins, or both? Circ Res. 2017 Sep 29;121(8):920–922. PubMed PMID: 28963190.
   PubMed Web of Science ®Google Scholar
• Kipps E, Tan DS, Kaye SB. Meeting the challenge of ascites in ovarian cancer: new avenues for therapy and research. Nat Rev Cancer. 2013 Apr;13(4):273–282. . PubMed PMID: 23426401.
   PubMed Web of Science ®Google Scholar
• Karimi N, Cvjetkovic A, Jang SC, et al. Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins. Cell Mol Life Sci. 2018 Aug;75(15):2873–2886. 10.1007/s00018-018-2773-4. PubMed PMID: 29441425; PubMed Central PMCID: PMC6021463.
   PubMed Web of Science ®Google Scholar