{"id":2391,"date":"2016-02-25T14:30:11","date_gmt":"2016-02-25T19:30:11","guid":{"rendered":"https:\/\/blogs.nature.com\/methagora\/?p=2391"},"modified":"2016-02-25T14:30:12","modified_gmt":"2016-02-25T19:30:12","slug":"methods-and-probes-for-cleared-tissue-an-imperfect-table","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/methagora\/2016\/02\/methods-and-probes-for-cleared-tissue-an-imperfect-table.html","title":{"rendered":"Methods and probes for cleared tissue: an imperfect table"},"content":{"rendered":"
\"TF<\/a>

{credit}Digital Vision\/Punchstock {\/credit}<\/p><\/div>\n

In the March issue of Nature Methods<\/em>, the technology feature explores some ways that labs are optimizing probes to image cleared tissue<\/a>. As we interviewed scientists, we learned about published work and ongoing unpublished experiences. Here is a snapshot of how some probes work with some clearing methods. It\u2019s an imperfect table and is likely to evolve as research continues. We welcome your comments. We know there are different viewpoints and varying experiences and we hope it will be helpful to others to hear about them.<\/p>\n

We wish this could be a wiki page, then again that might deprive you of your nighttime rest, as you edit one another\u2019s entries. This way, your comments can be seen by all.<\/p>\n

 <\/p>\n\n\n\n\n\n\n\n\n\n\n\n
An imperfect table about some labels that have been used in cleared tissue<\/strong><\/caption>\n
Probe<\/strong><\/th>\nLabeling shown in large samples<\/strong>b<\/sup><\/th>\nLabeling shown in small samples<\/strong><\/th>\nDoes not work well?<\/th>\n<\/tr>\n
Genetically encoded fluorescent proteins<\/strong><\/td>\n3DISCO<\/span> (signal quenched after a few days), CLARITY<\/span>, CUBIC<\/span>, ExM<\/span> (variant)a<\/sup>, PACT\/PARS<\/span> (signal retained 6 months and longer)a<\/sup>, sDISCO<\/span>a<\/sup><\/td>\nBABB<\/span> (signal quenched after a few hours), ClearT2<\/span>, ExM<\/span> (variant)a<\/sup> , ExM\/ePACT<\/span>a<\/sup> , Scal<\/em>eA2<\/span>, Scal<\/em>eS<\/span>, SeeDB<\/span>,
\nSucrose<\/span>, TDE<\/span><\/td>\n		<\/td>\n<\/tr>\n
Immunolabels<\/strong><\/td>\n3DISCO<\/span>, CLARITY<\/span>, iDISCO<\/span>, iDISCO+<\/span>a<\/sup>, iSeeDB<\/span>, PACT\/PARS<\/span>, Sucrose<\/span>, SWITCH<\/span><\/td>\nBABB<\/span>, ClearT<\/span>, ClearT2<\/span>, CUBIC<\/span>, SeeDB<\/span>, SeeDB2<\/span>a<\/sup> (in press) Sucrose<\/span>, TDE<\/span>, ExM<\/span><\/td>\n<\/td>\n<\/tr>\n
Specific nucleic acid detection<\/strong><\/td>\nEDC-CLARITY<\/span><\/td>\nCLARITY<\/span>, ExM<\/span> (variant)a<\/sup>, PACT\/PARS<\/span><\/td>\n<\/td>\n<\/tr>\n
Dyes and stains<\/strong><\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Congo Red<\/td>\n3DISCO<\/span><\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Lipophilic dyes such as DiI, Sudan Black<\/td>\nPACT\/PARS<\/span> (Sudan Black), SWITCH<\/span> (DiI)<\/td>\nClearT<\/span>, Scal<\/em>eS<\/span>, SeeDB<\/span><\/td>\n<\/td>\n<\/tr>\n
Nuclear stains such as DAPI, DRAQ5, SYTO and PI<\/td>\nCUBIC<\/span>, ExM<\/span> (variant)a<\/sup>, PACT\/PARS<\/span>, SWITCH<\/span><\/td>\nSeeDB<\/span>, SeeDB2<\/span>a<\/sup><\/td>\n<\/td>\n<\/tr>\n
SNAP-tags with SiR probes<\/td>\nPACT\/PARS<\/span>, BABB<\/span>, Scal<\/em>e<\/span><\/td>\nSeeDB<\/span><\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Clearing method: Solvent-based<\/strong><\/span>; simple immersion<\/strong><\/span>; hyperhydration<\/strong><\/span>; hydrogel-based<\/span>.<\/strong><\/p>\n

a<\/sup>Unpublished information<\/p>\n

b<\/sup>Indicates larger samples such as whole organs<\/p>\n

Sources: E. Boyden, MIT; K. Chung, MIT, K. Deisseroth, Stanford University; H-U. Dodt, Vienna University of Technology\/Medical University of Vienna; V. Gradinaru, Caltech; P. Heppenstall, EMBL; Takeshi Imai, RIKEN; \u00ad\u00adK. Johnsson, EPFL; J. Lichtman, D. Richardson, Harvard University; A. Miyawaki, RIKEN; M. Tessier-Lavigne, N. Renier, Rockefeller University.<\/p>\n

*<\/p>\n

Glossary of some tissue clearing agent acronyms<\/strong><\/p>\n

3DISCO :\u00a0 Three-dimensional imaging of solvent-cleared organs<\/p>\n

sDISCO: Stabilized three-dimensional imaging of solvent-cleared organs<\/p>\n

BABB :\u00a0 Benzyl alcohol and benzyl-benzoate<\/p>\n

CLARITY : Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging\/Immunostaining\/In situ hybridization-compatible Tissue-hYdrogel<\/p>\n

CUBIC : Clear unobstructed brain imaging cocktails and computational analysis<\/p>\n

EDC-CLARITY : 1-Ethyl-3-3-dimethyl-aminopropyl carbodiimide-CLARITY<\/p>\n

ePACT: PACT-based expansion clearing.<\/p>\n

iDISCO : Immunolabeling-enabled 3D imaging of solvent-cleared organs<\/p>\n

iDISCO+ : Immunolabeling-enabled 3D imaging of solvent-cleared organs\u00a0plus<\/p>\n

PACT :\u00a0 Passive Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging\/Immunostaining\/In situ hybridization-compatible Tissue-hYdrogel<\/p>\n

PARS : P<\/em>erfusion-assisted a<\/em>gent r<\/em>elease in s<\/em>itu<\/p>\n

SeeDB : See Deep Brain<\/p>\n

Spalteholz\u2019s preparation :\u00a0 Benzylbanzoate\/methylsalicate<\/p>\n

TDE\u00a0 : 2,2\u2032-thiodiethanol<\/p>\n

 <\/p>\n

Some lab resource pages <\/strong><\/p>\n

Chung lab resources<\/a> \u2013 Literature, protocols, videos and discussion pages from the MIT lab of Kwanghun Chung related to SWITCH, electrostochastic transport and CLARITY.<\/p>\n

CLARITY Resources<\/a> \u2013 Protocols, literature, data and videos related to CLARITY, developed in the lab of Karl Deisseroth at Stanford University. Links to CLARITY Wiki<\/a> and CLARITY Forum<\/a><\/p>\n

Expansion microscopy resources<\/a> \u2013 Literature and protocols related to expansion microscopy developed in the MIT lab of Edward Boyden.<\/p>\n

iDISCO resources<\/a> \u2013 Literature, protocols and information about validated antibodies related to iDISCO<\/p>\n

SeeDB Resources<\/a> \u2013 Protocols, literature videos related to SeeDB developed in the RIKEN lab of Takeshi Imai.<\/p>\n","protected":false},"excerpt":{"rendered":"

In the March issue of Nature Methods, the technology feature explores some ways that labs are optimizing probes to image cleared tissue. As we interviewed scientists, we learned about published work and ongoing unpublished experiences. Here is a snapshot of how some probes work with some clearing methods. It\u2019s an imperfect table and is likely to evolve as research continues. We welcome your comments. We know there are different viewpoints and varying experiences and we hope it will be helpful to others to hear about them.  Read more<\/a> Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":99,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-2391","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts\/2391","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/users\/99"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/comments?post=2391"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts\/2391\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/media?parent=2391"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/categories?post=2391"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/tags?post=2391"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}