'''Tissue clearing''' refers to a group of chemical techniques used to turn tissues transparent.<ref name=":0">{{cite journal | vauthors = Zhao J, Lai HM, Qi Y, He D, Sun H | title = Current Status of Tissue Clearing and the Path Forward in Neuroscience | journal = ACS Chemical Neuroscience | volume = 12 | issue = 1 | pages = 5–29 | date = January 2021 | pmid = 33326739 | doi = 10.1021/acschemneuro.0c00563 | s2cid = 229300600 }}</ref><ref name=":1" /><ref name=":3">{{cite journal | vauthors = Vigouroux RJ, Belle M, Chédotal A | title = Neuroscience in the third dimension: shedding new light on the brain with tissue clearing | journal = Molecular Brain | volume = 10 | issue = 1 | article-number = 33 | date = July 2017 | pmid = 28728585 | pmc = 5520295 | doi = 10.1186/s13041-017-0314-y | doi-access = free }}</ref> By turning tissues transparent to certain [[wavelengths]] of light, it allows one to gain optical access to a tissue.<ref name=":0" /> That is, light can pass into and out of the cleared tissue freely, allowing one to see the structures deep within the tissue without physically cutting it open. Many tissue clearing methods exist, each with different strengths and weaknesses.<ref name=":1" /><ref name=":4">{{cite journal | vauthors = Porter DD, Morton PD | title = Clearing techniques for visualizing the nervous system in development, injury, and disease | journal = Journal of Neuroscience Methods | volume = 334 | article-number = 108594 | date = January 2020 | pmid = 31945400 | doi = 10.1016/j.jneumeth.2020.108594 | s2cid = 210430342 | pmc = 10674098 }}</ref> Some are generally applicable, while others are designed for specific applications.<ref name=":4" /> Tissue clearing is usually useful only combined with one or more [[fluorescence | fluorescent]] labeling techniques such as [[immunolabeling]] and subsequently imaged, most often by [[optical sectioning]] microscopy techniques.<ref name=":0" /><ref name=":5">{{cite journal | vauthors = Tian T, Li X | title = Applications of tissue clearing in the spinal cord | journal = The European Journal of Neuroscience | volume = 52 | issue = 9 | pages = 4019–4036 | date = November 2020 | pmid = 32794596 | doi = 10.1111/ejn.14938 | s2cid = 221121163 }}</ref><ref name=":6">{{cite journal | vauthors = Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ | title = Tissue clearing and its applications in neuroscience | journal = Nature Reviews. Neuroscience | volume = 21 | issue = 2 | pages = 61–79 | date = February 2020 | pmid = 31896771 | doi = 10.1038/s41583-019-0250-1| pmc=8121164 | s2cid = 209528204 }}</ref> Tissue clearing has been applied to many areas in biological research.<ref name=":10">{{cite journal | vauthors = Gómez-Gaviro MV, Sanderson D, Ripoll J, Desco M | title = Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease | language = English | journal = iScience | volume = 23 | issue = 8 | article-number = 101432 | date = August 2020 | pmid = 32805648 | pmc = 7452225 | doi = 10.1016/j.isci.2020.101432 | bibcode = 2020iSci...23j1432G }}</ref> It is one of the more efficient ways to perform three-dimensional [[histology]].
== History == In the early 1900s, [[Werner Spalteholz]] developed a technique that allowed the clarification of large tissues,<ref name=":1">{{cite journal | vauthors = Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ | title = Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy | journal = Neuron | volume = 106 | issue = 3 | pages = 369–387 | date = May 2020 | pmid = 32380050 | pmc = 7213014 | doi = 10.1016/j.neuron.2020.03.004 }}</ref><ref name=":2">{{cite journal | vauthors = Azaripour A, Lagerweij T, Scharfbillig C, Jadczak AE, Willershausen B, Van Noorden CJ | title = A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue | journal = Progress in Histochemistry and Cytochemistry | volume = 51 | issue = 2 | pages = 9–23 | date = August 2016 | pmid = 27142295 | doi = 10.1016/j.proghi.2016.04.001 | doi-access = free }}</ref> using Wintergrünöl ([[methyl salicylate]]) and [[benzyl benzoate]].<ref>{{Cite book| vauthors = Spalteholz W |title=Über das Durchsichtigmachen von menschlichen und tierischen Präparaten und seine theoretischen Bedingungen, nebst Anhang: Über Knochenfärbung|publisher=S. Hirzel|year=1914|location=Leipzig}}</ref> Various scientists then introduced their own variations on Spalteholz's technique.<ref name=":2" /> Tuchin et al. introduced tissue optical clearing (TOC) in 1997, adding a new branch of tissue clearing that was [[Hydrophile|hydrophilic]] instead of hydrophobic like Spalteholz's technique.<ref name=":0" /><ref>{{cite journal | vauthors = Tuchin VV, Maksimova IL, Zimnyakov DA, Kon IL, Mavlyutov AH, Mishin AA | title = Light propagation in tissues with controlled optical properties | journal = Journal of Biomedical Optics | volume = 2 | issue = 4 | pages = 401–17 | date = October 1997 | pmid = 23014964 | doi = 10.1117/12.281502 | bibcode = 1997JBO.....2..401T | doi-access = free }}</ref> In the 1980s, Andrew Murray & [[Marc Kirschner]] developed a two-step process, wherein tissues were first dehydrated with [[Alcohol (chemistry)|alcohol]] and subsequently made transparent by immersion in a mixture of [[benzyl alcohol]] and [[benzyl benzoate]] (BABB), a technique they coupled with [[light sheet fluorescence microscopy]],<ref>{{cite journal |last1=Dent |last2=Polson |last3=Klymkowsky |title=A whole-mount immunocytochemical analysis of the expression of the intermediate filament protein vimentin in Xenopus |journal=Development |date=1989 |volume=105 |issue=1 |pages=61–74 |doi=10.1242/dev.105.1.61 |pmid=2806118 }}</ref><ref name=":1" /><ref name=":3" /> which remains the method with the highest clearing efficacy to date, regardless any tissue pre-processing step.<ref>{{cite journal |last1=Pan |first1=Chenchen |last2=Cai |first2=Ruiyao |last3=Quacquarelli |first3=Francesca Paola |last4=Ghasemigharagoz |first4=Alireza |last5=Lourbopoulos |first5=Athanasios |last6=Matryba |first6=Paweł |last7=Plesnila |first7=Nikolaus |last8=Dichgans |first8=Martin |last9=Hellal |first9=Farida |last10=Ertürk |first10=Ali |title=Shrinkage-mediated imaging of entire organs and organisms using uDISCO |journal=Nature Methods |date=2016 |volume=13 |issue=10 |pages=859–867 |doi=10.1038/nmeth.3964 |pmid=27548807 }}</ref> In the most extreme case, it allows the clearing of a whole [[mouse]] of even a whole human [[brain]].<ref>{{cite journal |last1=Zhao |first1=Shan |last2=Mihail Ivilinov |first2=Todorov |last3=Ruiyao |first3=Cai |last4=Rami |first4=AI -Maskari |last5=Hanno |first5=Steinke |last6=Elisabeth |first6=Kemter |last7=Hongcheng |first7=Mai |last8=Zhouyi |first8=Rong |last9=Martin |first9=Warmer |last10=Karen |first10=Stanic |last11=Oliver |first11=Schoppe |last12=Johannes Christian |first12=Paetzold |last13=Benno |first13=Gesierich |last14=Milagros N. |first14=Wong |last15=Tobias B. |first15=Huber |last16=Marco |first16=Duering |last17=Oliver Thomas |first17=Bruns |last18=Bjoern |first18=Menze |last19=Jan |first19=Lipfert |title=Cellular and Molecular Probing of Intact Human Organs |journal=Cell |date=2020 |volume=2020 |issue=4 |pages=796–812.e19 |doi=10.1016/j.cell.2020.01.030 |pmid=32059778 |pmc=7557154 }}</ref>
In 2024, Hong, Brongersma, and Ou reported that applying high concentrations of the food dye [[tartrazine]] could transiently and reversibly increase the optical transparency of certain biological tissues, including the skin, in live mice.<ref>{{Cite journal |last1=Ou |first1=Zihao |last2=Duh |first2=Yi-Shiou |last3=Rommelfanger |first3=Nicholas J. |last4=Keck |first4=Carl H. C. |last5=Jiang |first5=Shan |last6=Brinson |first6=Kenneth |last7=Zhao |first7=Su |last8=Schmidt |first8=Elizabeth L. |last9=Wu |first9=Xiang |last10=Yang |first10=Fan |last11=Cai |first11=Betty |last12=Cui |first12=Han |last13=Qi |first13=Wei |last14=Wu |first14=Shifu |last15=Tantry |first15=Adarsh |date=2024-09-06 |title=Achieving optical transparency in live animals with absorbing molecules |journal=Science |volume=385 |issue=6713 |article-number=eadm6869 |doi=10.1126/science.adm6869 |pmc=11931656 |pmid=39236186 |bibcode=2024Sci...385m6869O }}</ref><ref>{{Cite journal |last1=Keck |first1=Carl H. C. |last2=Schmidt |first2=Elizabeth Lea |last3=Zhao |first3=Su |last4=Liu |first4=Zhongyu |last5=Zhang |first5=Ling-Yi |last6=Cui |first6=Miao |last7=Chen |first7=Xiaoyu |last8=Wang |first8=Chonghe |last9=Cui |first9=Han |last10=Brongersma |first10=Mark L. |last11=Hong |first11=Guosong |date=2025-05-13 |title=Achieving transient and reversible optical transparency in live mice with tartrazine |url=https://www.nature.com/articles/s41596-025-01187-z |journal=Nature Protocols |volume=21 |issue=1 |language=en |pages=319–346 |doi=10.1038/s41596-025-01187-z |pmid=40360854 |issn=1750-2799}}</ref><ref>{{Cite journal |last1=Shabbir |first1=Muhammad Waqas |last2=Asante-Asare |first2=David |last3=Phillips |first3=Matthew |last4=Ou |first4=Zihao |date=2025-07-11 |title=Transient Optical Clearing Using Absorbing Molecules for Ex Vivo and In Vivo Imaging |url=https://app.jove.com/t/68629/transient-optical-clearing-using-absorbing-molecules-for-ex-vivo-vivo |journal=Journal of Visualized Experiments |language=en |issue=221 |article-number=e68629 |doi=10.3791/68629 |pmid=40720350 |issn=1940-087X}}</ref> The authors attributed this effect to tartrazine's strong absorption in the blue region of the visible [[Electromagnetic spectrum|spectrum]] and to [[refractive index]] modulation at longer wavelengths, consistent with the [[Kramers–Kronig relations]]. Following publication, the findings have been independently reproduced and extended by multiple laboratories in several subsequent studies.<ref name=":15">{{Cite journal |last1=Miller |first1=David A. |last2=Xu |first2=Yirui |last3=Highland |first3=Robert |last4=Nguyen |first4=Van Tu |last5=Brown |first5=William J. |last6=Hong |first6=Guosong |last7=Yao |first7=Junjie |last8=Wax |first8=Adam |date=2025-01-20 |title=Enhanced penetration depth in optical coherence tomography and photoacoustic microscopy in vivo enabled by absorbing dye molecules |url=https://opg.optica.org/abstract.cfm?URI=optica-12-1-24 |journal=Optica |language=en |volume=12 |issue=1 |pages=24–30 |doi=10.1364/OPTICA.546779 |pmid=41625956 |pmc=12858289 |bibcode=2025Optic..12...24M |issn=2334-2536}}</ref><ref name=":16">{{Cite journal |last1=Surkov |first1=Y. |last2=Timoshina |first2=P. |last3=Uvakin |first3=I. |last4=Shushunova |first4=N. |last5=Konovalov |first5=A. |last6=Kozlov |first6=I. |last7=Piavchenko |first7=G. |last8=Telyshev |first8=D. |last9=Meglinski |first9=I. |last10=Kuznetsov |first10=S. |last11=Tuchin |first11=V. |date=2025-10-16 |title=Computer-guided optical clearing for transcranial laser speckle imaging of cortical blood flow through synergistic tartrazine-induced cranial bone transparency |url=https://www.worldscientific.com/doi/10.1142/S1793545825400024 |journal=Journal of Innovative Optical Health Sciences |article-number=2540002 |doi=10.1142/S1793545825400024 |issn=1793-5458}}</ref><ref>{{cite bioRxiv|last1=Tie |first1=Xin |title=Absorbing molecules make both abdomen and back transparent in live mice |date=2024-11-01 |language=en |biorxiv=10.1101/2024.10.28.620537 |last2=Sun |first2=Ting |last3=Xiao |first3=Guixiu |last4=Zhao |first4=Yanjie |last5=Su |first5=Jing |last6=Xie |first6=Xiaoqi |last7=Yin |first7=Wanhong}}</ref><ref name=":17">{{Cite journal |last1=Zuo |first1=Tianxiang |last2=Tao |first2=Chao |last3=Liu |first3=Xiaojun |date=2025-04-01 |title=Absorbing molecules as optical clearing agents improve the resolution and sensitivity of photoacoustic microscopy |url=https://opg.optica.org/abstract.cfm?URI=ol-50-7-2282 |journal=Optics Letters |language=en |volume=50 |issue=7 |pages=2282–2285 |doi=10.1364/OL.555723 |pmid=40167701 |bibcode=2025OptL...50.2282Z |issn=0146-9592}}</ref> Specifically, this ''in vivo'' optical clearing approach has been applied by multiple independent laboratories to enhance imaging depth in modalities such as [[optical coherence tomography]] and [[photoacoustic imaging]].<ref name=":15" /><ref name=":17" /><ref>{{Cite journal |last1=Jia |first1=Conger |last2=Zhang |first2=Zhiling |last3=Shen |first3=Yuecheng |last4=Hou |first4=Wanli |last5=Zhao |first5=Jiayu |last6=Luo |first6=Jiawei |last7=Chen |first7=Haoran |last8=Qi |first8=Dalong |last9=Yao |first9=Yunhua |last10=Deng |first10=Lianzhong |last11=Ma |first11=Hongmei |last12=Sun |first12=Zhenrong |last13=Zhang |first13=Shian |date=2025-06-01 |title=Tartrazine-enabled optical clearing for in vivo optical resolution photoacoustic microscopy |url=https://opg.optica.org/abstract.cfm?URI=boe-16-6-2504 |journal=Biomedical Optics Express |language=en |volume=16 |issue=6 |pages=2504–2515 |doi=10.1364/BOE.565643 |pmid=40677379 |pmc=12265485 |issn=2156-7085}}</ref><ref>{{Cite journal |last1=Xu |first1=Maoyuan |last2=Yang |first2=Bingqian |last3=Song |first3=Shen |last4=Xu |first4=Tianpeng |last5=Yao |first5=Jinyu |last6=Liu |first6=Yuehao |last7=Cui |first7=Yaoyao |last8=Zhang |first8=Yachao |date=2025-10-01 |title=Multi-wavelength photoacoustic microscopy enhanced by the high-sensitivity probe and reversible tissue transparent molecules |url=https://opg.optica.org/abstract.cfm?URI=prj-13-10-2757 |journal=Photonics Research |language=en |volume=13 |issue=10 |page=2757 |doi=10.1364/PRJ.565972 |issn=2327-9125}}</ref><ref>{{Cite journal |last1=Liang |first1=Yilin |last2=Meng |first2=Xiaochen |last3=Wang |first3=Chongyang |last4=Ma |first4=Jiawei |last5=Zhang |first5=Xuanye |last6=Fan |first6=Fan |last7=Zhu |first7=Jiang |date=September 2025 |title=Optical Coherence Tomography and Angiography Image Enhancement Using Optical Clearing Agent Tartrazine |url=https://onlinelibrary.wiley.com/doi/10.1002/jbio.202500297 |journal=Journal of Biophotonics |volume=19 |issue=1 |article-number=e202500297 |language=en |doi=10.1002/jbio.202500297 |pmid=40890078 |issn=1864-063X}}</ref><ref>{{Cite journal |last1=Narawane |first1=Amit |last2=Trout |first2=Robert |last3=Viehland |first3=Christian |last4=Kuo |first4=Anthony N. |last5=Vajzovic |first5=Lejla |last6=Dhalla |first6=Al-Hafeez |last7=Toth |first7=Cynthia A. |date=2024-12-09 |title=Optical clearing with tartrazine enables deep transscleral imaging with optical coherence tomography |journal=Journal of Biomedical Optics |volume=29 |issue=12 |doi=10.1117/1.JBO.29.12.120501 |pmid=39669907 |pmc=11635458 |bibcode=2024JBO....29l0501N |issn=1083-3668}}</ref> In 2025, Valery V. Tuchin, a pioneer in hydrophilic tissue clearing, demonstrated tartrazine can make the skull more transparent in live mice, enabling transcranial laser [[speckle imaging]] of cortical blood flow in real time.<ref name=":16" /> In addition, a number of other labs have demonstrated the utility of tartrazine to enable deep-tissue [[Raman spectroscopy|Raman sensing]]<ref>{{Cite journal |last1=Lee |first1=Michael Ka Ho |last2=Mizushima |first2=Kenta |last3=Zheng |first3=Peng |last4=Tanwar |first4=Swati |last5=Gupta |first5=Anoushka |last6=Fujita |first6=Katsumasa |last7=Barman |first7=Ishan |date=2025-10-24 |title=Spectrally Silent and Optically Transparent: Clear-SiR for Deep Raman Biomolecular Sensing |journal=ACS Sensors |volume=10 |issue=10 |pages=7702–7711 |doi=10.1021/acssensors.5c02046 |pmid=41024637 |pmc=12993836 |bibcode=2025ACSSe..10.7702L }}</ref> and [[Fluorescence-lifetime imaging microscopy|fluorescence lifetime imaging]].<ref>{{Cite journal |last1=Yuan |first1=Nanxue |last2=Ragab |first2=Saif |last3=Chavez |first3=Luis |last4=Pandey |first4=Vikas |last5=Intes |first5=Xavier |date=2025-12-15 |title=Evaluating tartrazine as an optical clearing agent for fluorescence lifetime imaging |url=https://opg.optica.org/abstract.cfm?URI=ol-50-24-7588 |journal=Optics Letters |language=en |volume=50 |issue=24 |pages=7588–7591 |doi=10.1364/OL.579040 |pmid=41396940 |bibcode=2025OptL...50.7588Y |issn=0146-9592}}</ref> In addition to tartrazine, several other absorbing dye molecules, including the FDA-approved contrast agents [[fluorescein]] and [[indocyanine green]], have also been repurposed to function as ''in vivo'' optical clearing agents.<ref>{{cite journal |last1=Trout |first1=Robert M |language=en |biorxiv=10.1101/2025.07.01.661162 |last2=Narawane |first2=Amit |last3=Viehland |first3=Christian |last4=Ownagh |first4=Vahid |last5=Draelos |first5=Mark |last6=Dhalla |first6=Al-Hafeez |last7=Kuo |first7=Anthony |last8=Toth |first8=Cynthia |title=Optical Coherence Tomography with Fluorescein Optical Clearing for Transscleral Image Guidance |journal=International Journal of Translational Medicine |date=2026 |volume=6 |page=7 |doi=10.3390/ijtm6010007 |doi-access=free }}</ref><ref>{{Cite journal |last1=Lu |first1=Kechao |last2=Xu |first2=Yirui |last3=Miller |first3=David A. |last4=Wang |first4=Wan |last5=Gupta |first5=Deven |last6=Yao |first6=Junjie |last7=Wax |first7=Adam |date=2025-09-01 |title=Indocyanine green (ICG) enhances penetration of 1300 nm optical coherence tomography imaging for in vivo murine skin |url=https://opg.optica.org/abstract.cfm?URI=ol-50-17-5226 |journal=Optics Letters |language=en |volume=50 |issue=17 |pages=5226–5229 |doi=10.1364/OL.569764 |pmid=40882048 |pmc=12848760 |bibcode=2025OptL...50.5226L |issn=0146-9592}}</ref><ref>{{Cite journal |last1=Keck |first1=Carl H. C. |last2=Schmidt |first2=Elizabeth L. |last3=Roth |first3=Richard H. |last4=Floyd |first4=Brendan M. |last5=Tsai |first5=Andy P. |last6=Garcia |first6=Hassler B. |last7=Cui |first7=Miao |last8=Chen |first8=Xiaoyu |last9=Wang |first9=Chonghe |last10=Park |first10=Andrew |last11=Zhao |first11=Su |last12=Liao |first12=Pinyu A. |last13=Casey |first13=Kerriann M. |last14=Reineking |first14=Wencke |last15=Cai |first15=Sa |date=2025-09-02 |title=Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice |journal=Proceedings of the National Academy of Sciences |volume=122 |issue=35 |article-number=e2504264122 |doi=10.1073/pnas.2504264122 |pmc=12415250 |pmid=40857313 |bibcode=2025PNAS..12204264K }}</ref> This observation suggests that the underlying physical principle of dye-enabled optical clearing is not limited to a single [[molecule]] and that multiple dye molecules may be repurposed as tissue clearing agents.
== Principles == Tissue opacity is thought to be the result of light scattering due to heterogeneous [[Refractive index|refractive indices]].<ref name=":0" /><ref name=":4" /><ref name=":5" /> Tissue clearing methods chemically homogenize refractive indices, resulting in almost completely transparent tissue.<ref name=":4" /><ref name=":6" />
== Classifications == While there are multiple class names for tissue-clearing methods, they are all classified based on the final state of the tissue by the end of the clearing method.<ref name=":0" /> These include hydrophobic clearing methods,<ref name=":0" /><ref name=":1" /><ref name=":6" /> which may also be known as organic,<ref name=":3" /> solvent-based,<ref name=":4" /><ref name=":5" /> organic solvent-based,<ref name=":7">{{cite journal | vauthors = Tian T, Yang Z, Li X | title = Tissue clearing technique: Recent progress and biomedical applications | journal = Journal of Anatomy | volume = 238 | issue = 2 | pages = 489–507 | date = February 2021 | pmid = 32939792 | pmc = 7812135 | doi = 10.1111/joa.13309 }}</ref><ref name=":8">{{cite journal | vauthors = Jing D, Yi Y, Luo W, Zhang S, Yuan Q, Wang J, Lachika E, Zhao Z, Zhao H | display-authors = 6 | title = Tissue Clearing and Its Application to Bone and Dental Tissues | journal = Journal of Dental Research | volume = 98 | issue = 6 | pages = 621–631 | date = June 2019 | pmid = 31009584 | pmc = 6535919 | doi = 10.1177/0022034519844510 }}</ref> or dehydration<ref name=":9">{{cite journal | vauthors = Watson AM, Watkins SC | title = Massive volumetric imaging of cleared tissue: The necessary tools to be successful | journal = The International Journal of Biochemistry & Cell Biology | volume = 112 | pages = 76–78 | date = July 2019 | pmid = 31085331 | doi = 10.1016/j.biocel.2019.05.007 | s2cid = 155088859 }}</ref> clearing methods; hydrophilic clearing methods,<ref name=":0" /><ref name=":1" /><ref name=":6" /> which may also be known as aqueous-based<ref name=":5" /><ref name=":7" /> or water-based<ref name=":9" /> methods, and hydrogel-based clearing methods.<ref name=":1" /><ref name=":0" />
== Labeling == Tissue clearing methods have varying compatibility with different methods of [[Fluorescent tag|fluorescent labeling]].<ref name=":0" /><ref name=":5" /><ref name=":6" /> Some are better suited to genetic labelling by endogenously expressed [[fluorescent protein]],<ref name=":0" /><ref name=":5" /> while others externally delivered probes as [[immunolabeling]] and chemical dye labeling.<ref name=":0" /><ref name=":5" /> The latter is more general and applicable to all tissues, notably human tissues, but the penetration of the probes becomes a critical problem.<ref>{{cite journal |last1=Yau |first1=Chun Ngo |last2=Hei Ming |first2=Lai |title=Principles of deep immunohistochemistry for 3D histology |journal=Cell Reports Methods |date=2023 |volume=3 |issue=5 |article-number=100458 |doi=10.1016/j.crmeth.2023.100458 |pmid=37323568 |pmc=10261851 }}</ref>
== Imaging == After clearing and labeling, tissues are typically imaged using [[confocal microscopy]],<ref name=":7" /><ref name=":8" /><ref name=":9" /> [[Two-photon excitation microscopy|two-photon microscopy]],<ref name=":0" /><ref name=":5" /><ref name=":7" /> or one of the many variants of [[Light sheet fluorescence microscopy|light-sheet fluorescence microscopy]].<ref name=":10" /><ref name=":7" /><ref name=":8" /> Other less commonly used methods include [[optical projection tomography]]<ref name=":0" /><ref name=":5" /> and [[Raman scattering|stimulated Raman scattering]].<ref name=":5" /><ref name=":10" /><ref name=":7" /> As long as the tissue allows for the unobstructed passing of light, the [[optical resolution]] is fundamentally limited by [[diffraction-limited system | Abbe diffraction limit]]. The compatibility of any tissue clearing method with any microscopy system is, therefore, configurational rather than optical.
== Data == Tissue clearing is one of the more efficient ways to facilitate 3D imaging of tissues, and hence generates massive volumes of complex data, which requires powerful computational hardware and software to store, process, analyze, and visualize.<ref name=":0" /><ref name=":6" /><ref name=":9" /> A single [[mouse brain]] can generate terabytes of data.<ref name=":1" /><ref name=":6" /><ref name=":9" /> Both commercial and open-source software exists to address this need, some of it adapted from solutions for two-dimensional images and some of it designed specifically for the three-dimensional images produced by imaging of cleared tissues.<ref name=":0" /><ref name=":7" /><ref name=":8" />
== Applications == Tissue clearing has been applied to the nervous system,<ref name=":0" /><ref name=":1" /><ref name=":3" /><ref name=":4" /><ref name=":5" /><ref name=":6" /><ref name=":10" /><ref name=":7" /><ref>{{cite journal | vauthors = Kumar V, Krolewski DM, Hebda-Bauer EK, Parsegian A, Martin B, Foltz M, Akil H, Watson SJ | display-authors = 6 | title = Optimization and evaluation of fluorescence in situ hybridization chain reaction in cleared fresh-frozen brain tissues | journal = Brain Structure & Function | volume = 226 | issue = 2 | pages = 481–499 | date = March 2021 | pmid = 33386994 | pmc = 7962668 | doi = 10.1007/s00429-020-02194-4 }}</ref><ref>{{cite journal | vauthors = Dai Z, Sun Y, Zhao X, Pu X | title = Novel imaging and related techniques for studies of diseases of the central nervous system: a review | journal = Cell and Tissue Research | volume = 380 | issue = 3 | pages = 415–424 | date = June 2020 | pmid = 32072308 | doi = 10.1007/s00441-020-03183-z | s2cid = 211170939 }}</ref> bones (including teeth),<ref name=":10" /><ref name=":7" /><ref name=":8" /><ref>{{cite journal | vauthors = Greenbaum A, Chan KY, Dobreva T, Brown D, Balani DH, Boyce R, Kronenberg HM, McBride HJ, Gradinaru V | display-authors = 6 | title = Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow | journal = Science Translational Medicine | volume = 9 | issue = 387 | article-number = eaah6518 | date = April 2017 | pmid = 28446689 | doi = 10.1126/scitranslmed.aah6518 | s2cid = 8799170 | url = https://resolver.caltech.edu/CaltechAUTHORS:20161221-135116035 }}</ref><ref>{{cite book | vauthors = Treweek JB, Beres A, Johnson N, Greenbaum A | title = Skeletal Development and Repair | chapter = Phenotyping Intact Mouse Bones Using Bone CLARITY | series = Methods in Molecular Biology | volume = 2230 | pages = 217–230 | date = 2021 | pmid = 33197017 | doi = 10.1007/978-1-0716-1028-2_13 | publisher = Springer US | isbn = 978-1-0716-1028-2 | s2cid = 226988513 | place = New York, NY | veditors = Hilton MJ }}</ref><ref name=":11">{{cite journal | vauthors = Wang HM, Khoradmehr A, Tamadon A, Velez E, Nabipour I, Jokar N, Assadi M, Gholamrezanezhad A | display-authors = 6 | title = Imaging of the muscle and bone from benchtop to bedside | journal = European Review for Medical and Pharmacological Sciences | volume = 24 | issue = 6 | pages = 3254–3266 | date = March 2020 | pmid = 32271443 | doi = 10.26355/eurrev_202003_20693 | s2cid = 215602325 }}</ref> skeletal muscles,<ref name=":10" /><ref name=":11" /><ref>{{cite journal | vauthors = Li Y, Xu J, Zhu J, Yu T, Zhu D | title = Three-dimensional visualization of intramuscular innervation in intact adult skeletal muscle by a modified iDISCO method | journal = Neurophotonics | volume = 7 | issue = 1 | article-number = 015003 | date = January 2020 | pmid = 32016132 | pmc = 6977403 | doi = 10.1117/1.NPh.7.1.015003 }}</ref> hearts and vasculature,<ref name=":10" /><ref name=":7" /><ref>{{cite journal | vauthors = Olianti C, Costantini I, Giardini F, Lazzeri E, Crocini C, Ferrantini C, Pavone FS, Camici PG, Sacconi L | display-authors = 6 | title = 3D imaging and morphometry of the heart capillary system in spontaneously hypertensive rats and normotensive controls | journal = Scientific Reports | volume = 10 | issue = 1 | article-number = 14276 | date = August 2020 | pmid = 32868776 | pmc = 7459314 | doi = 10.1038/s41598-020-71174-9 | bibcode = 2020NatSR..1014276O }}</ref> gastrointestinal organs,<ref name=":10" /><ref>{{cite journal | vauthors = Liu CY, Polk DB | title = Cellular maps of gastrointestinal organs: getting the most from tissue clearing | journal = American Journal of Physiology. Gastrointestinal and Liver Physiology | volume = 319 | issue = 1 | pages = G1–G10 | date = July 2020 | pmid = 32421359 | pmc = 7468759 | doi = 10.1152/ajpgi.00075.2020 }}</ref> urogenital organs,<ref name=":10" /><ref name=":7" /><ref>{{cite journal | vauthors = Isaacson D, McCreedy D, Calvert M, Shen J, Sinclair A, Cao M, Li Y, McDevitt T, Cunha G, Baskin L | display-authors = 6 | title = Imaging the developing human external and internal urogenital organs with light sheet fluorescence microscopy | journal = Differentiation; Research in Biological Diversity | volume = 111 | pages = 12–21 | date = 2020-01-01 | pmid = 31634681 | doi = 10.1016/j.diff.2019.09.006 | s2cid = 204833112 | url = https://escholarship.org/uc/item/8d39b32q }}</ref> skin,<ref name=":10" /><ref>{{cite journal | vauthors = Fernandez E, Marull-Tufeu S | title = 3D imaging of human epidermis micromorphology by combining fluorescent dye, optical clearing and confocal microscopy | journal = Skin Research and Technology | volume = 25 | issue = 5 | pages = 735–742 | date = September 2019 | pmid = 31074525 | doi = 10.1111/srt.12710 | s2cid = 149445451 }}</ref> lymph nodes,<ref name=":10" /> mammary glands,<ref name=":10" /> lungs,<ref name=":10" /> eyes,<ref name=":10" /> tumors,<ref name=":10" /><ref name=":7" /> and adipose tissues.<ref name=":10" /><ref name=":7" /> Whole-body clearing is less common, but has been done in smaller animals, including rodents.<ref name=":0" /><ref name=":6" /><ref name=":10" /> Tissue clearing has also been applied to human cancer tissues.<ref name=":12">{{cite journal | vauthors = Tanaka N, Kanatani S, Tomer R, Sahlgren C, Kronqvist P, Kaczynska D, Louhivuori L, Kis L, Lindh C, Mitura P, Stepulak A, Corvigno S, Hartman J, Micke P, Mezheyeuski A, Strell C, Carlson JW, Fernández Moro C, Dahlstrand H, Östman A, Matsumoto K, Wiklund P, Oya M, Miyakawa A, Deisseroth K, Uhlén P | title = Whole-tissue biopsy phenotyping of three-dimensional tumours reveals patterns of cancer heterogeneity | language = English | journal = Nature Biomedical Engineering | volume = 1 | issue = 10 | pages = 796–806 | date = October 2017 | pmid = 31015588 | pmc = | doi = 10.1038/s41551-017-0139-0 | bibcode = | s2cid = 256713371 }}</ref><ref name=":13">{{cite journal | vauthors = Tanaka N, Kanatani S, Kaczynska D, Fukumoto K, Louhivuori L, Mizutani T, Kopper O, Kronqvist P, Robertson S, Lindh C, Kis L, Pronk R, Niwa N, Matsumoto K, Oya M, Miyakawa A, Falk A, Hartman J, Sahlgren C, Clevers H, Uhlén P | title = Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies | language = English | journal = Nature Biomedical Engineering | volume = 4 | issue = 9 | pages = 875–888 | date = September 2020 | pmid = 32601394 | pmc = | doi = 10.1038/s41551-020-0576-z | bibcode = | s2cid = 256704785 }}</ref> For some techniques, bone tissue must be [[Decalcify|decalcified]] to remove light-scattering [[hydroxyapatite]] crystals, leaving behind a [[Extracellular matrix|protein matrix]] suitable for clearing.<ref name=":14">{{cite journal |vauthors=Zhao J, Lai HM, Qi Y, He D, Sun H |date=January 2021 |title=Current Status of Tissue Clearing and the Path Forward in Neuroscience |journal=ACS Chemical Neuroscience |volume=12 |issue=1 |pages=5–29 |doi=10.1021/acschemneuro.0c00563 |pmid=33326739 |s2cid=229300600}}</ref><ref name=":32">{{cite journal |vauthors=Vigouroux RJ, Belle M, Chédotal A |date=July 2017 |title=Neuroscience in the third dimension: shedding new light on the brain with tissue clearing |journal=Molecular Brain |volume=10 |issue=1 |article-number=33 |doi=10.1186/s13041-017-0314-y |pmc=5520295 |pmid=28728585 |doi-access=free}}</ref>
== References == {{Reflist}}
[[Category:Tissue engineering]]