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Imaging and Analysis of Cellular Locations in Three-Dimensional Tissue Models

  • Warren Colomb (a1), Matthew Osmond (a2), Charles Durfee (a1), Melissa D. Krebs (a2) and Susanta K. Sarkar (a1)...

Abstract

The absence of quantitative in vitro cell–extracellular matrix models represents an important bottleneck for basic research and human health. Randomness of cellular distributions provides an opportunity for the development of a quantitative in vitro model. However, quantification of the randomness of random cell distributions is still lacking. In this paper, we have imaged cellular distributions in an alginate matrix using a multiview light sheet microscope and developed quantification metrics of randomness by modeling it as a Poisson process, a process that has constant probability of occurring in space or time. We imaged fluorescently labeled human mesenchymal stem cells embedded in an alginate matrix of thickness greater than 5 mm with $\sim\! {\rm 2}{\rm. 9} \pm {\rm 0}{\rm. 4}\,\mu {\rm m}$ axial resolution, the mean full width at half maximum of the axial intensity profiles of fluorescent particles. Simulated randomness agrees well with the experiments. Quantification of distributions and validation by simulations will enable quantitative study of cell–matrix interactions in tissue models.

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Corresponding author

*Author for correspondence: Susanta K. Sarkar, E-mail: ssarkar@mines.edu

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Ahrens, MB, Orger, MB, Robson, DN, Li, JM & Keller, PJ (2013). Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat Methods 10, 413420.
Alexander, N, Moyeed, R & Stander, J (2000). Spatial modelling of individual-level parasite counts using the negative binomial distribution. Biostatistics 1, 453463.
Andersen, T, Auk-Emblem, P & Dornish, M (2015). 3D cell culture in alginate hydrogels. Microarrays 4, 133161.
Andrey, P, Kiêu, K, Kress, C, Lehmann, G, Tirichine, L, Liu, Z, Biot, E, Adenot, P-G, Hue-Beauvais, C & Houba-Hérin, N (2010). Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 6, e1000853.
Baddeley, A, Moyeed, R, Howard, C & Boyde, A (1993). Analysis of a three-dimensional point pattern with replication. Appl Stat 4, 641668.
Baddeley, A, Rubak, E & Turner, R (2015). Spatial Point Patterns: Methodology and Applications with R. Florida, USA: CRC Press.
Barkai, N & Leibler, S (2000). Biological rhythms: Circadian clocks limited by noise. Nature 403, 267268.
Beaurepaire, E (2014). Laboratoire Optique et Biosciences-Two-photon light sheet microscopy (2P-SPIM). Nat Methods 11, 600601.
Berg, OG, Paulsson, J & Ehrenberg, M (2000). Fluctuations and quality of control in biological cells: Zero-order ultrasensitivity reinvestigated. Biophys J 79, 12281236.
Bidarra, SJ & Barrias, CC (2018). 3D Culture of Mesenchymal Stem Cells in Alginate Hydrogels. In: Methods in Molecular Biology. New York, USA: Humana Press.
Bielecka, ZF, Maliszewska-Olejniczak, K, Safir, IJ, Szczylik, C & Czarnecka, AM (2017). Three-dimensional cell culture model utilization in cancer stem cell research. Biol Rev 92, 15051520.
Breslin, S & O'Driscoll, L (2013). Three-dimensional cell culture: The missing link in drug discovery. Drug Discov Today 18, 240249.
Bumb, A, Sarkar, SK, Wu, XS, Brechbiel, MW & Neuman, KC (2011). Quantitative characterization of fluorophores in multi-component nanoprobes by single-molecule fluorescence. Biomed Opt Express 2, 27612769.
Caló, E & Khutoryanskiy, VV (2015). Biomedical applications of hydrogels: A review of patents and commercial products. Eur Polym J 65, 252267.
Chen, B-C, Legant, WR, Wang, K, Shao, L, Milkie, DE, Davidson, MW, Janetopoulos, C, Wu, XS, Hammer, JA & Liu, Z (2014). Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998.
Chung, K & Deisseroth, K (2013). CLARITY for mapping the nervous system. Nat Methods 10, 508513.
Dean, KM & Fiolka, R (2014). Uniform and scalable light-sheets generated by extended focusing. Opt Express 22, 2614126152.
Decaestecker, C, Debeir, O, Van Ham, P & Kiss, R (2007). Can anti-migratory drugs be screened in vitro? A review of 2D and 3D assays for the quantitative analysis of cell migration. Med Res Rev 27, 149176.
Diggle, PJ (2013). Statistical Analysis of Spatial and Spatio-Temporal Point Patterns. Florida, USA: CRC Press.
Elliott, NT & Yuan, F (2011). A review of three-dimensional in vitro tissue models for drug discovery and transport studies. J Pharm Sci 100, 5974.
Fahrbach, FO, Voigt, FF, Schmid, B, Helmchen, F & Huisken, J (2013). Rapid 3D light-sheet microscopy with a tunable lens. Opt Express 21, 2101021026.
Gao, L, Shao, L, Chen, B-C & Betzig, E (2014). 3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy. Nat Protoc 9, 10831101.
Gillespie, DT (1977). Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81, 23402361.
Green, RH (1966). Measurement of non-randomness in spatial distributions. Res Popul Ecol (Kyoto) 8, 17.
Hama, H, Kurokawa, H, Kawano, H, Ando, R, Shimogori, T, Noda, H, Fukami, K, Sakaue-Sawano, A & Miyawaki, A (2011). Scale: A chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat Neurosci 14, 14811488.
Hinderer, S, Layland, SL & Schenke-Layland, K (2016). ECM and ECM-like materials—biomaterials for applications in regenerative medicine and cancer therapy. Adv Drug Delivery Rev 97, 260269.
Horton, NG, Wang, K, Kobat, D, Clark, CG, Wise, FW, Schaffer, CB & Xu, C (2013). In vivo three-photon microscopy of subcortical structures within an intact mouse brain. Nat Photonics 7, 205209.
Huang, F, Sirinakis, G, Allgeyer, ES, Schroeder, LK, Duim, WC, Kromann, EB, Phan, T, Rivera-Molina, FE, Myers, JR & Irnov, I (2016). Ultra-high resolution 3D imaging of whole cells. Cell 166, 10281040.
Illian, J, Penttinen, A, Stoyan, H & Stoyan, D (2008). Statistical Analysis and Modelling of Spatial Point Patterns. New Jersey, USA: John Wiley & Sons.
Keller, PJ & Dodt, H-U (2012). Light sheet microscopy of living or cleared specimens. Curr Opin Neurobiol 22, 138143.
Keller, PJ, Schmidt, AD, Santella, A, Khairy, K, Bao, Z, Wittbrodt, J & Stelzer, EH (2010). Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat Methods 7, 637642.
Keller, PJ, Schmidt, AD, Wittbrodt, J & Stelzer, EH (2008). Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 10651069.
König, K (2000). Multiphoton microscopy in life sciences. J Microsc 200, 83104.
Krzic, U, Gunther, S, Saunders, TE, Streichan, SJ & Hufnagel, L (2012). Multiview light-sheet microscope for rapid in toto imaging. Nat Methods 9, 730733.
Levene, MJ, Dombeck, DA, Kasischke, KA, Molloy, RP & Webb, WW (2004). In vivo multiphoton microscopy of deep brain tissue. J Neurophysiol 91, 19081912.
Mahou, P, Vermot, J, Beaurepaire, E & Supatto, W (2014). Multicolor two-photon light-sheet microscopy. Nat Methods 11, 600601.
Maia, FR, Fonseca, KB, Rodrigues, G, Granja, PL & Barrias, CC (2014). Matrix-driven formation of mesenchymal stem cell–extracellular matrix microtissues on soft alginate hydrogels. Acta Biomater 10, 31973208.
Marycz, K, Szarek, D, Grzesiak, J & Wrzeszcz, K (2014). Influence of modified alginate hydrogels on mesenchymal stem cells and olfactory bulb-derived glial cells cultures. Bio-Med Mater Eng 24, 16251637.
Mertz, J (2011). Optical sectioning microscopy with planar or structured illumination. Nat Methods 8, 811819.
Mertz, J & Kim, J (2010) Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection. J Biomed Opt 15, 016027-1–016027-7.
Mlodzianoski, MJ, Juette, MF, Beane, GL & Bewersdorf, J (2009). Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy. Opt Express 17, 82648277.
Nicodemus, GD & Bryant, SJ (2008). Cell encapsulation in biodegradable hydrogels for tissue engineering applications. Tissue Eng, Part B 14, 149165.
Ozbudak, EM, Thattai, M, Kurtser, I, Grossman, AD & Van Oudenaarden, A (2002). Regulation of noise in the expression of a single gene. Nat Genet 31, 6973.
Pan, C, Cai, R, Quacquarelli, FP, Ghasemigharagoz, A, Lourbopoulos, A, Matryba, P, Plesnila, N, Dichgans, M, Hellal, F & Ertürk, A (2016). Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat Methods 13, 859867.
Pertuz, S, Puig, D, Garcia, MA & Fusiello, A (2013). Generation of all-in-focus images by noise-robust selective fusion of limited depth-of-field images. IEEE Trans Image Process 22, 12421251.
Pittenger, MF, Mackay, AM, Beck, SC, Jaiswal, RK, Douglas, R, Mosca, JD, Moorman, MA, Simonetti, DW, Craig, S & Marshak, DR (1999). Multilineage potential of adult human mesenchymal stem cells. Science 284, 143147.
Planchon, TA, Gao, L, Milkie, DE, Davidson, MW, Galbraith, JA, Galbraith, CG & Betzig, E (2011). Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat Methods 8, 417423.
Preibisch, S, Saalfeld, S, Schindelin, J & Tomancak, P (2010). Software for bead-based registration of selective plane illumination microscopy data. Nat Methods 7, 418419.
Preibisch, S, Saalfeld, S & Tomancak, P (2009). Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25, 14631465.
Qiao, S-P, Zhao, Y-F, Li, C-F, Yin, Y-B, Meng, Q-Y, Lin, F-H, Liu, Y, Hou, X-L, Guo, K & Chen, X-B (2016). An alginate-based platform for cancer stem cell research. Acta Biomater 37, 8392.
Ragan, T, Kadiri, LR, Venkataraju, KU, Bahlmann, K, Sutin, J, Taranda, J, Arganda-Carreras, I, Kim, Y, Seung, HS & Osten, P (2012). Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat Methods 9, 255258.
Reynaud, EG, Kržič, U, Greger, K & Stelzer, EH (2008). Light sheet-based fluorescence microscopy: More dimensions, more photons, and less photodamage. HFSP J 2, 266275.
Ripley, BD (1976). The second-order analysis of stationary point processes. J Appl Probab 13, 255266.
Ripley, BD (1977). Modelling spatial patterns. Journal of the Royal Statistical Society. Series B (Methodological) 1977 (Jan 1), 172212.
Ritter, JG, Spille, J-H, Kaminski, T & Kubitscheck, U (2011). A cylindrical zoom lens unit for adjustable optical sectioning in light sheet microscopy. Biomed Opt Express 2, 185193.
Ritter, JG, Veith, R, Veenendaal, A, Siebrasse, JP & Kubitscheck, U (2010). Light sheet microscopy for single molecule tracking in living tissue. PLoS ONE 5, e11639.
Robinson, BK, Cortes, E, Rice, AJ, Sarper, M & del Río Hernández, A (2016). Quantitative analysis of 3D extracellular matrix remodelling by pancreatic stellate cells. Biol Open 0, 18. doi:10.1242/bio.017632.
Rodriguez, A, Ehlenberger, D, Kelliher, K, Einstein, M, Henderson, SC, Morrison, JH, Hof, PR & Wearne, SL (2003). Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 30, 94105.
Rowley, JA, Madlambayan, G & Mooney, DJ (1999). Alginate hydrogels as synthetic extracellular matrix materials. Biomaterials 20, 4553.
Ruedinger, F, Lavrentieva, A, Blume, C, Pepelanova, I & Scheper, T (2015). Hydrogels for 3D mammalian cell culture: A starting guide for laboratory practice. Appl Microbiol Biotechnol 99, 623636.
Sarkar, SK (2016). Single Molecule Biophysics and Poisson Process Approach to Statistical Mechanics. California, USA: Morgan & Claypool Publishers.
Sbalzarini, IF & Koumoutsakos, P (2005). Feature point tracking and trajectory analysis for video imaging in cell biology. J Struct Biol 151, 182195.
Shapiro, L & Cohen, S (1997). Novel alginate sponges for cell culture and transplantation. Biomaterials 18, 583590.
Silvestri, L, Allegra Mascaro, AL, Costantini, I, Sacconi, L & Pavone, FS (2014). Correlative two-photon and light sheet microscopy. Methods 66, 268272.
Summers, HD, Wills, JW, Brown, MR & Rees, P (2015). Poisson-event-based analysis of cell proliferation. Cytometry Part A 87, 385392.
Susaki, EA, Tainaka, K, Perrin, D, Kishino, F, Tawara, T, Watanabe, TM, Yokoyama, C, Onoe, H, Eguchi, M & Yamaguchi, S (2014). Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726739.
Tibbitt, MW & Anseth, KS (2009). Hydrogels as extracellular matrix mimics for 3D cell culture. Biotechnol Bioeng 103, 655663.
Till, JE, McCulloch, EA & Siminovitch, L (1964). A stochastic model of stem cell proliferation, based on the growth of spleen colony-forming cells. Proc Natl Acad Sci USA 51, 2936.
Tinevez, J-Y, Perry, N, Schindelin, J, Hoopes, GM, Reynolds, GD, Laplantine, E, Bednarek, SY, Shorte, SL & Eliceiri, KW (2017). Trackmate: An open and extensible platform for single-particle tracking. Methods 115, 8090.
Tomer, R, Khairy, K, Amat, F & Keller, PJ (2012). Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods 9, 755763.
Tsimring, LS (2014). Noise in biology. Rep Prog Phys 77, 026601.
Vettenburg, T, Dalgarno, HI, Nylk, J, Coll-Lladó, C, Ferrier, DE, Čižmár, T, Gunn-Moore, FJ & Dholakia, K (2014). Light-sheet microscopy using an Airy beam. Nat Methods 11, 541544.
Wearne, S, Rodriguez, A, Ehlenberger, D, Rocher, A, Henderson, S & Hof, P (2005). New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 136, 661680.
Weber, M, Mickoleit, M & Huisken, J (2013). Light sheet microscopy. Methods Cell Biol 123, 193215.
Weiswald, L-B, Bellet, D & Dangles-Marie, V (2015). Spherical cancer models in tumor biology. Neoplasia 17, 115.
Wu, Y, Wawrzusin, P, Senseney, J, Fischer, RS, Christensen, R, Santella, A, York, AG, Winter, PW, Waterman, CM & Bao, Z (2013). Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol 31, 10321038.
Yang, X, Sarvestani, SK, Moeinzadeh, S, He, X & Jabbari, E (2012). Three-dimensional-engineered matrix to study cancer stem cells and tumorsphere formation: Effect of matrix modulus. Tissue Eng, Part A 19, 669684.
Zipfel, WR, Williams, RM & Webb, WW (2003). Nonlinear magic: Multiphoton microscopy in the biosciences. Nat Biotechnol 21, 13691377.
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Microscopy and Microanalysis
  • ISSN: 1431-9276
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