Application of clearing methods on tissues in the three-dimensional imaging research

doi:10.16098/j.issn.0529-1356.2018.03.022

Abstract

Abstract:

With the development of the microscopy and the big data acquisition processing system, the research direction gradually becomes the construction of biological structures by 3D imaging. However, because of opaque which leads to scattering of imaging light through the tissues, the depth of the imaging becomes a challenge. A technique named “clearing” can increase the organization transparency so that they can enhance the depth of the imaging and have a three-dimensional reconstruction. Being hydrophilic, the clearing reagents were divided into solvent-based clearing and aqueous-based clearing. The solvent-based clearing reduced water in the tissue and aqueous-based clearing used the hydration shell made by water to keep the fluorescent protein stability. In this article we introduced different clearing method and compared them from clearing time and retention in the fluorescence.

Key words: Clearing, Microscopy imaging, Three-dimensional reconstruction, Lipid removal, Fluorescent stability

LI Ying-ze SHAO Zhi-hua LI Si-guang. Application of clearing methods on tissues in the three-dimensional imaging research[J]. Acta Anatomica Sinica, 2018, 49(3): 400-405.

References

［1］Richardson DS, Lichtman JW. Clarifying tissue clearing［J］. Cell, 2015, 162(2): 246-257.

［2］Micheva KD1, Smith SJ. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits［J］. Neuron, 2007, 55(1): 25-36.

［3］Denk W, Strickler JH, Webb WW. Two-photon laser scanning fluorescence microscopy［J］. Science, 1990, 248(4951): 73-76.

［4］Adams MW, Loftus AF, Dunn SE, et al. Light sheet fluorescence microscopy (LSFM) ［J］. Curr Protoc Cytom, 2015, 71: 1-15.

［5］Erturk A, Becker K, Jahrling N，et al. Three-dimensional imaging of solvent-cleared organs using 3DISCO［J］. Nat Protoc, 2012, 7(11): 1983-1995.

［6］Steinke H, Wolff W. A modified Spalteholz technique with preservation of the histology［J］. Ann Anat, 2001, 183(1): 91-95.

［7］Dodt HU, Leischner U, Schierloh A, et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain［J］. Nat Methods, 2007, 4(4): 331-336.

［8］Kolesova H, Capek M, Radochova B, et al. Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts［J］. Histochem Cell Biol, 2016, 146(2): 141-152.

［9］Parra SG, Chia TH, Zinter JP, et al. Multiphoton microscopy of cleared mouse organs［J］. J Biomed Opt, 2010, 15(3): 036017.

［10］Erturk A, Mauch CP, Hellal F, et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury［J］. Nat Med, 2011, 18(1): 166-171.

［11］Renier N, Wu Z, Simon DJ, et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging［J］. Cell, 2014, 159(4): 896-910.

［12］Seo J, M Choe, Kim SY. Clearing and labeling techniques for large-scale biological tissues［J］. Mol Cells, 2016, 39(6): 439-446.

［13］Tsai PS, Kaufhold JP, Blinder P, et al. Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels［J］. J Neurosci, 2009, 29(46): 14553-14570.

［14］Lin HH, Lai JS, Chin AL,et al. A map of olfactory representation in the drosophila mushroom body［J］. Cell, 2007, 128(6): 1205-1217.

［15］Chiang AS, Lin WY, Liu HP, et al. Insect NMDA receptors mediate juvenile hormone biosynthesis［J］. Proc Natl Acad Sci USA, 2002, 99(1): 37-42.

［16］Moy AJ, Capulong BV, Saager RB, et al. Optical properties of mouse brain tissue after optical clearing with FocusClear［J］. J Biomed Opt, 2015, 20(9): 95010.

［17］Kuwajima T, Sitko AA, Bhansali P, et al. ClearT: a detergent-and solvent-free clearing method for neuronal and non-neuronal tissue［J］. Development, 2013, 140(6): 1364-1368.

［18］Ke MT, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction［J］. Nat Neurosci, 2013, 16(8): 1154-1161.

［19］Ke MT, Imai T. Optical clearing of fixed brain samples using SeeDB［J］. Curr Protoc Neurosci, 2014, 66: Unit 2.22.

［20］Ke MT, Nakai Y, Fujimoto S, et al. Super-resolution mapping of neuronal circuitry with an index-optimized clearing agent［J］. Cell Rep, 2016, 14(11): 2718-2732.

［21］Hou B, Zhang D, Zhao S, et al. Scalable and DiI-compatible optical clearance of the mammalian brain［J］. Front Neuroanat, 2015, 9: 19.

［22］Costantini I, Ghobril JP, Di Giovanna AP, et al. A versatile clearing agent for multi-modal brain imaging［J］. Sci Rep, 2015, 5: 9808.

［23］Hama H, Kurokawa H, Kawano H, et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain［J］. Nat Neurosci, 2011, 14(11): 1481-1488.

［24］Hama H, Hioki H, Namiki K, et al. ScaleS: an optical clearing palette for biological imaging［J］. Nat Neurosci, 2015, 18(10): 1518-1529.

［25］Susaki EA, Tainaka K, Perrin D, et al. Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging［J］. Nat Protoc, 2015, 10(11): 1709-1727.

［26］Tainaka K, Kubota SI, Suyama TQ, et al. Whole-body imaging with single-cell resolution by tissue decolorization［J］. Cell, 2014, 159(4): 911-924.

［27］Fumoto S, Nishimura K, Nishida K, et al. Three-dimensional imaging of the intracellular fate of plasmid dna and transgene expression: zsgreen1 and tissue clearing method cubic are an optimal combination for multicolor deep imaging in murine tissues［J］. PLoS One, 2016, 11(1): e0148233.

［28］Tomer R, Ye L, Hsueh B, et al. Advanced CLARITY for rapid and high-resolution imaging of intact tissues［J］. Nat Protoc, 2014, 9(7): 1682-1697.

［29］Epp JR, Niibori Y, Liz Hsiang HL, et al. Optimization of CLARITY for clearing whole-brain and other intact organs(1,2,3) ［J］. JoVE, 2015, 2(3):1-15.

［30］Yang B, Treweek JB, Kulkarni RP, et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing［J］. Cell, 2014, 158(4): 945-958.

［31］Roberts DG, Johnsonbaugh HB, Spence RD, et al. Optical clearing of the mouse central nervous system using passive CLARITY［J］. J Vis Exp, 2016(112):1-9.

[32] Lee E,Choi J,Jo Y,et al.ACT-PRESTO:rapid and consistent tissue clearing and labeling methpd for 3-dimensional (3D)imaging[J].Sci rep,2016,6:18631.

[1]	YANG Yang SHI Jun LI Kun MA Yuan ZHANG Shao-jie HOU Er-fei WANG Chao-qun CHEN Jie WANG Xing LI Zhi-jun. Finite element analysis of cervical intervertebral discs after removing different ranges of uncinate processes [J]. Acta Anatomica Sinica, 2024, 55(1): 88-97.
[2]	MI Si-rong LIU Guang-xing ZHANG Zhen-wu YU Peng-hui JU Xiao-jun RAO Li-bing LI Li . Accuracy of 3D printing skull under different CT layer thickness [J]. Acta Anatomica Sinica, 2023, 54(5): 575-581.
[3]	ZHONG Hua WANG Ying FAN Ying-lei REN Hai-long PEMA Dor-ji TONG Qing-hua. Linear measurement of digital pelvic of normal Tibetan nationality female in Lhasa [J]. Acta Anatomica Sinica, 2023, 54(4): 460-464.
[4]	GUO Lan-qian WANG Ding-xuan YI Gang LI Yan REN Jie-ying . Morphological classification and clinical significance of the coracoid process based on CT three-dimensional reconstruction [J]. Acta Anatomica Sinica, 2023, 54(1): 82-86.
[5]	DENG Si-qi GU Ling WANG Kai-yue CHEN Hong-yu LIU Yu-jie ZHANG Jie ZHAI Xiao-yue. Three-dimensional visualization on the relationship between tubules after macula densa and afferent arterioles in mouse kidney [J]. Acta Anatomica Sinica, 2023, 54(1): 87-91.
[6]	ZHANG Lei LI Zhi-qing TANG Xiao-gao ZHOU Xin LI Bing-kun FU Shi-jie. Anatomic classification of the sustentaculum tali and its characteristics analysis [J]. Acta Anatomica Sinica, 2022, 53(4): 515-519.
[7]	ZHANG Yin-ping WU Fei YU Hui TANG Yao ZHANG Hui CHEN Wei . Clinical application of imaging anatomy of pulmonary vessels in segmental pulmonary resection [J]. Acta Anatomica Sinica, 2022, 53(2): 217-224.
[8]	RUAN Cai-lian GUO Hong-tao HUI Xue-feng WANG Lu ZHU Hui ZHAO Lin LIU Bo-feng LI Xiao-ji. Morphological analysis of thoracic pedicle of 12-15-year-old idiopathic scoliosis and normal spine in northern Shaanxi province [J]. Acta Anatomica Sinica, 2022, 53(2): 225-237.
[9]	MA Yu-bo CHEN Juan ZHAI Xiao-qiang ZHANG Tong-dian CHONG Tie WANG Zi-ming ZHAO Jun. Three-dimensional reconstruction and anatomy of human epididymal duct [J]. Acta Anatomica Sinica, 2021, 52(6): 960-965.
[10]	CONG Jing GU Ling ZHANG Jie SONG Ke-xin ZHAI Xia-yue WANG Xiao-jie. Three-dimensional visualization of the renal proximal tubules in developing mice [J]. Acta Anatomica Sinica, 2021, 52(5): 789-794.
[11]	HU Ding-xiang LI Chang-hui CHEN Liang MA Chen-xi HUANG He ZHENG Rui-qing. Morphological classification and clinical significance of inferior angle of scapula based on CT three-dimensional reconstruction [J]. Acta Anatomica Sinica, 2021, 52(5): 767-771.
[12]	WU Li-bing GAO Shang XU Yang-yang WANG Yi-dan HE Yu-jie WANG Hai-yan LI Xiao-he LI Zhi-jun. Comparison of the effect between virtual simulation operation and conventional operation for the treatment of kidney stones [J]. Acta Anatomica Sinica, 2021, 52(4): 609-617.
[13]	WU Chao WANG Yi-dan GUAN Huan-huan GAO Ming-jie ZHANG Yun-feng WANG Hai-yan HE Yu-jie GAO Shang LI Zhi-jun LI Xiao-he . Three-dimensional digital measurement of occipital condyle and foramen magnum in Inner Mongolia [J]. Acta Anatomica Sinica, 2021, 52(1): 84-90.
[14]	XU Xue-bin WANG Xing LI Kun LI Xiao-he QU Xing-yue WEI Yu ZHANG Shao-jie LI Zhi-jun. Data set and visualization of continuous thin layer specimen of Chinese preschool boys#br# [J]. Acta Anatomica Sinica, 2020, 51(6): 924-928.
[15]	AN Feng-yang WANG Yu-hui SUN Jian-bin LI Li-juan TIAN Ge ZHU Li LUO Yan-lin. Relationship between optic nerve and sinuses based on 3D reconstruction of head and neck CT angiography [J]. Acta Anatomica Sinica, 2020, 51(5): 644-652.