Procedures for the quantification of whole-tissue immunofluorescence images obtained at single-cell resolution during murine tubular organ development

PLoS ONE

Volumn 10, Issue 8, 2015, Pages

  Hirashima, Tsuyoshi ^a   Adachi, Taiji ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

F ACTIN; UVOMORULIN; FIXATIVE;

ANTIBODY LABELING; ARTICLE; CONTROLLED STUDY; DIGITAL IMAGING; EMBRYO; EPIDIDYMIS; EPITHELIUM CELL; FEASIBILITY STUDY; FEMALE; IMAGE PROCESSING; IMMUNOFLUORESCENCE; KIDNEY; LUNG; MALE; MICROSCOPY; MITOSIS; MORPHOGENESIS; MOUSE; NONHUMAN; ORGANOGENESIS; ANIMAL; CHEMISTRY; DEVICES; FLUORESCENCE IMAGING; GROWTH, DEVELOPMENT AND AGING; MAMMALIAN EMBRYO; METABOLISM; PHYSIOLOGY; PROCEDURES; SINGLE CELL ANALYSIS; STATISTICS AND NUMERICAL DATA; THREE DIMENSIONAL IMAGING; TISSUE FIXATION; ULTRASTRUCTURE;

ANIMALS; EMBRYO, MAMMALIAN; EPIDIDYMIS; FIXATIVES; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; KIDNEY; LUNG; MALE; MICE; MITOSIS; OPTICAL IMAGING; ORGANOGENESIS; SINGLE-CELL ANALYSIS; TISSUE FIXATION;

EID: 84942474510     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0135343     Document Type: Article

References (31)

1. Keller PJ. Imaging morphogenesis: technological advances and biological insights. Science. 2013; 340: 1234168. doi: 10.1126/science.1234168 PMID: 23744952
2. Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, et al. Visualization of image data from cells to organisms. Nat Methods. 2010; 7: S26-S41. doi: 10.1038/nmeth0610-479a PMID: 20195255
3. Megason SG, Fraser SE. Imaging in Systems Biology. Cell. 2007. pp. 784-795. doi: 10.1016/j.cell. 2007.08.031
4. Packard A, Georgas K, Michos O, Riccio P, Cebrian C, Combes AN, et al. Luminal Mitosis Drives Epithelial Cell Dispersal within the Branching Ureteric Bud. Dev Cell. 2013; 27: 319-330. doi: 10.1016/j. devcel.2013.09.001 PMID: 24183650
5. Tang N, Marshall WF, McMahon M, Metzger RJ, Martin GR. Control of mitotic spindle angle by the RAS-regulated ERK1/2 pathway determines lung tube shape. Science (80-). 2011; 333: 342-345. doi: 10.1126/science.1204831
6. Long F, Zhou J, Peng H. Visualization and analysis of 3D microscopic images. PLoS Comput Biol. 2012;8. doi: 10.1371/journal.pcbi.1002519
7. Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nature Neuroscience. 2011. pp. 1481-1488. doi: 10.1038/nn.2928 PMID: 21878933
8. Yokomizo T, Yamada-Inagawa T, Yzaguirre AD, Chen MJ, Speck NA, Dzierzak E. Whole-mount threedimensional imaging of internally localized immunostained cells within mouse embryos. Nat Protoc. 2012; 7: 421-431. doi: 10.1038/Nprot.2011.441 PMID: 22322215
9. Dent JA, Polson AG, Klymkowsky MW. A whole-mount immunocytochemical analysis of the expression of the intermediate filament protein vimentin in Xenopus. Development. 1989; 105: 61-74. PMID: 2806118
10. Ke M-T, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat Neurosci. 2013; 16: 1154-61. doi: 10.1038/nn.3447 PMID: 23792946
11. Chung K, Wallace J, Kim S-Y, Kalyanasundaram S, Andalman AS, Davidson TJ, et al. Structural and molecular interrogation of intact biological systems. Nature. 2013; 497: 332-7. doi: 10.1038/nature12107 PMID: 23575631
12. Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, et al. Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing. Cell. 2014. doi: 10.1016/j.cell.2014.07. 017
13. Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell. 2014; 157: 726-739. doi: 10.1016/j.cell.2014.03.042 PMID: 24746791
14. Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, et al. Whole-body imaging with single-cell resolution by tissue decolorization. Cell. 2014; 159, 911-924. doi: 10.1016/j.cell.2014. 10.034 PMID: 25417165
15. Ahrens MB, Orger MB, Robson DN, Li JM, Keller PJ. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat Methods. 2013; 10: 413-420. doi: 10.1038/nmeth.2434 PMID: 23524393
16. Krzic U, Gunther S, Saunders TE, Streichan SJ, Hufnagel L. Multiview light-sheet microscope for rapid in toto imaging. Nature Methods. 2012. pp. 730-733. doi: 10.1038/nmeth.2064 PMID: 22660739
17. Truong T V, Supatto W, Koos DS, Choi JM, Fraser SE. Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat Methods. 2011; 8: 757-760. doi: 10.1038/nmeth.1652 PMID: 21765409
18. Michael L, Sweeney DE, Davies JA. A role for microfilament-based contraction in branching morphogenesis of the ureteric bud. Kidney International. 2005. pp. 2010-2018. doi: 10.1111/j.1523-1755. 2005.00655.x PMID: 16221201
19. Cho EA, Patterson LT, Brookhiser WT, Mah S, Kintner C, Dressler GR. Differential expression and function of cadherin-6 during renal epithelium development. Development. 1998; 125: 803-812. PMID: 9449663
20. Rosenberg P, Esni F, Sjödin A, Larue L, Carlsson L, Gullberg D, et al. A potential role of R-cadherin in striated muscle formation. Dev Biol. 1997; 187: 55-70. doi: 10.1006/dbio.1997.8602 PMID: 9224674
21. Rock JR, Hogan BLM. Epithelial progenitor cells in lung development, maintenance, repair, and disease. Annu Rev Cell Dev Biol. 2011; 27: 493-512. doi: 10.1146/annurev-cellbio-100109-104040 PMID: 21639799
22. Hirashima T. Pattern formation of an epithelial tubule by mechanical instability during epididymal development. Cell Reports. 2014; 9: 866-873. doi: 10.1016/j.celrep.2014.09.041 PMID: 25437543
23. Hayashi K, Yonemura S, Matsui T, Tsukita S. Immunofluorescence detection of ezrin/radixin/moesin (ERM) proteins with their carboxyl-terminal threonine phosphorylated in cultured cells and tissues. J Cell Sci. 1999; 112 (Pt 8: 1149-1158.
24. Shindo A, Wallingford JB. PCP and septins compartmentalize cortical actomyosin to direct collective cell movement. Supplementary Data. Science. 2014; 343: 649-52. doi: 10.1126/science.1243126 PMID: 24503851
25. Guillot C, Lecuit T. Mechanics of epithelial tissue homeostasis and morphogenesis. Science. 2013; 340: 1185-9. doi: 10.1126/science.1235249 PMID: 23744939
26. CardosoWV, Lü J. Regulation of early lung morphogenesis: questions, facts and controversies. Development. 2006; 133: 1611-1624. doi: 10.1242/dev.02310 PMID: 16613830
27. Short K, Hodson M, Smyth I. Spatial mapping and quantification of developmental branching morphogenesis. Development. 2013; 140: 471-478. doi: 10.1242/dev.088500 PMID: 23193168
28. Jackson M, Taylor a H, Jones E a, Forrester LM. Mouse Cell Culture. Methods Mol Biol. 2010; 633: 29-56.
29. Lin C, Su W, Li L. Heat-Induced Antigen Retrieval Applied in Zebrafish: Whole-Mount In Situ Immunofluorescence Microscopy. Microscopy and Microanalysis. 2012. pp. 493-496. doi: 10.1017/S1431927612000141 PMID: 22640961
30. Kapur JN, Sahoo PK, Wong AKC. A new method for gray-level picture thresholding using the entropy of the histogram. Computer Vision, Graphics, and Image Processing. 1985. p. 140. doi: 10.1016/S0734-189X(85)90156-2
31. Gonzalez RC, Woods RE. Digital Image Processing [Internet]. Development. 2007. doi: 10.1007/3-540-27563-0