Selected articles:

Nat Protoc. 2015 Nov;10(11):1709-27. doi: 10.1038/nprot.2015.085. Epub 2015 Oct 8.
Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.
Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, Ueda HR.

Exp Eye Res. 2015 Oct;139:136-43. doi: 10.1016/j.exer.2015.06.008. Epub 2015 Jun 11.
Combined 3DISCO clearing method, retrograde tracer and ultramicroscopy to map corneal neurons in a whole adult mouse trigeminal ganglion.
Launay PS, Godefroy D, Khabou H, Rostene W, Sahel JA, Baudouin C, Melik Parsadaniantz S, Reaux-Le Goazigo A.

DOI: 10.1523/ENEURO.0022-15.2015
Optimization of CLARITY for Clearing Whole-Brain and Other Intact Organs
Jonathan R. Epp, Yosuke Niibori, Hwa-Lin (Liz) Hsiang, Valentina Mercaldo, Karl Deisseroth, Sheena A. Josselyn, Paul W. Frankland.

Blood. 2015 Jun 11;125(24):3769-77. doi: 10.1182/blood-2014-09-603803. Epub 2015 Apr 23.
Podoplanin and CLEC-2 drive cerebrovascular patterning and integrity during development.
Lowe KL, Finney BA, Deppermann C, Hägerling R, Gazit SL, Frampton J, Buckley C, Camerer E, Nieswandt B, Kiefer F, Watson SP.

PLoS One. 2015 Apr 7;10(4):e0122976. doi: 10.1371/journal.pone.0122976. eCollection 2015.
A transgenic Prox1-Cre-tdTomato reporter mouse for lymphatic vessel research.
Bianchi R, Teijeira A, Proulx ST, Christiansen AJ, Seidel CD, Rülicke T, Mäkinen T, Hägerling R, Halin C, Detmar M.

eneuro; DOI: 10.1523/ENEURO.0001-15.2015
3D imaging of axons in transparent spinal cords from rodents and non-human primates      
Soderblom C, Lee DH, Dawood A, Carballosa M, Santamaria AJ, Benavides FD, Jergova S, Grumbles R, Thomas C, Park K, Guest JD, Lemmon V, Lee JK, Tsoulfas P. 

Cell. 2014 Nov 6;159(4):896-910
iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging.
Renier N, Wu Z, Simon DJ, Yang J, Ariel P, Tessier-Lavigne M.

Cell. 2014 Nov 6;159(4):911-24
Whole-body imaging with single-cell resolution by tissue decolorization.
Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, Ukai H, Ueda HR.

Cell Rep. 2014 Nov 20;9(4):1191-201.
A Simple Method for 3D Analysis of Immunolabeled Axonal Tracts in a Transparent Nervous System.
Belle M, Godefroy D, Dominici C, Heitz-Marchaland C, Zelina P, Hellal F,  Bradke F, Chédotal A

Mol Cell Biol. 2014 May;34(9):1634-48. doi: 10.1128/MCB.01526-13. Epub 2014 Feb 24.
Fusing VE-cadherin to α-catenin impairs fetal liver hematopoiesis and lymph but not blood vessel formation.
Dartsch N, Schulte D, Hägerling R, Kiefer F, Vestweber D.

Cell. 2014 Apr 24

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis
Susaki EA, Tainaka K, Perrin, Kishino F, Tawara T, Watanabe TM, Yokoyama C, Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H, Ueda HR.

Cancer Res. 2014 Apr
Apoptosis Imaging for Monitoring DR5 Antibody Accumulation and Pharmacodynamics in Brain Tumors Noninvasively
Weber TG, Osl F, Renner A, Pöschinger T, Galbán S, Rehemtulla A, Scheuer W.

Invest Radiol. 2014 Mar
Dynamic Contrast-Enhanced Micro-Computed Tomography Correlates With 3-Dimensional Fluorescence Ultramicroscopy in Antiangiogenic Therapy of Breast Cancer Xenografts
Pöschinger T, Renner A, Eisa F, Dobosz M, Strobel S, Weber TG, Brauweiler R, Kalender WA, Scheuer W.

Neoplasia. 2014 Jan
Multispectral fluorescence ultramicroscopy: three-dimensional visualization and automatic quantification of tumor morphology, drug penetration, and antiangiogenic treatment response
Dobosz M, Ntziachristos V, Scheuer W, Strobel S

The EMBO Journal. 2013 May
A novel multistep mechanism for initial lymphangiogenesis in mouse embryos based on ultramicroscopy
René Hägerling, Cathrin Pollmann, Martin Andreas, Christian Schmidt, Harri Nurmi, Ralf H Adams, Kari Alitalo, Volker Andresen, Stefan Schulte-Merker and Friedemann Kiefer

Experimental Neurology. 2013 Mar

Three-dimensional evaluation of retinal ganglion cell axon regeneration and pathfinding in whole mouse tissue after injury
Luo, X., Salgueiro, Y., Beckerman, S. R., Lemmon, V. P., Tsoulfas, P., & Park, K. K.

Nature protocols. 2012 Oct
Three-dimensional imaging of solvent-cleared organs using 3DISCO
Ali Ertürk, Klaus Becker, Nina Jährling, Christoph P Mauch, Caroline D Hojer, Jackson G Egen, Farida Hellal, Frank Bradke, Morgan Sheng & Hans-Ulrich Dodt