Recent developments in automated optical sectioning microscope systems have enabled
researchers to conduct high resolution, three-dimensional (3D) microscopy at the scale
of millimeters in various types of tissues. This powerful technology allows the exploration
of tissues at an unprecedented level of detail, while preserving the spatial context.
By doing so, such technology will also enable researchers to explore cellular and
molecular signatures within tissue and correlate with disease course. This will allow
an improved understanding of pathophysiology and facilitate a precision medicine approach
to assess the response to treatment. The ability to perform large-scale imaging in
3D cannot be realized without the widespread availability of accessible quantitative
analysis. In this review, we will outline recent advances in large-scale 3D imaging
and discuss the available methodologies to perform meaningful analysis and potential
applications in translational research.
Abbreviations:
2D (2 dimensional), 3D (3 dimensional), LSM (Light sheet microscopy), IHCS (imaging high content screening), VTEA (Volumetric tissue exploration and analysis), 3DTC (3 dimensional tissue cytometry)To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Translational ResearchAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- Protocol biopsy of the stable renal transplant: a multicenter study of methods and complication rates.Transplantation. 2003; 76: 969-973
- Prognostic impact of microvasculopathy on survival after heart transplantation: evidence from 9713 endomyocardial biopsies.Circulation. 2007; 116: 1274-1282
- Estrogen receptor and progesterone receptor as predictive biomarkers of response to endocrine therapy: a prospectively powered pathology study in the Tamoxifen and Exemestane Adjuvant Multinational trial.J Clin Oncol. 2011; 29: 1531-1538
- Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer.J Clin Oncol. 1999; 17: 1474-1481
- American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer.J Clin Oncol. 2007; 25: 5287-5312
- Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.Proc Natl Acad Sci U S A. 2001; 98: 10869-10874
- Tamm-Horsfall protein translocates to the basolateral domain of thick ascending limbs, interstitium, and circulation during recovery from acute kidney injury.Am J Physiol Ren Physiol. 2013; 304: F1066-F1075
- Tamm-Horsfall protein-deficient thick ascending limbs promote injury to neighboring S3 segments in an MIP-2-dependent mechanism.Am J Physiol Ren Physiol. 2011; 300: F999-1007
- Tamm-Horsfall protein protects the kidney from ischemic injury by decreasing inflammation and altering TLR4 expression.Am J Physiol Ren Physiol. 2008; 295: F534-F544
- Quantitative three-dimensional tissue cytometry to study kidney tissue and resident immune cells.J Am Soc Nephrol. 2017; 28: 2108-2118
- Multiphoton microscopy with clearing for three dimensional histology of kidney biopsies.Biomed Opt Express. 2016; 7: 3089-3096
- Tetrahydrofuran (THF) for routine dehydration, clearing, and infiltration.Am J Clin Pathol. 1959; 31: 357-361
- Clarifying tissue clearing.Cell. 2015; 162: 246-257
- SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction.Nat Neurosci. 2013; 16: 1154-1161
- Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.Nat Protoc. 2015; 10: 1709-1727
- ScaleS: an optical clearing palette for biological imaging.Nat Neurosci. 2015; 18: 1518-1529
- High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO).Exp Neurol. 2013; 242: 57-64
- iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging.Cell. 2014; 159: 896-910
- Simple, scalable proteomic imaging for high-dimensional profiling of intact systems.Cell. 2015; 163: 1500-1514
- Structural and molecular interrogation of intact biological systems.Nature. 2013; 497: 332-337
- Single-cell phenotyping within transparent intact tissue through whole-body clearing.Cell. 2014; 158: 945-958
- ACT-PRESTO: rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging.Sci Rep. 2016; 6: 18631
- Advanced CLARITY for rapid and high-resolution imaging of intact tissues.Nat Protoc. 2014; 9: 1682-1697
- Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts.Histochem Cell Biol. 2016; 146: 141-152
- Handbook of biological confocal microscopy.3rd ed. Springer, New York, NY2006
- Preservation of biological specimens for observation in a confocal fluorescence microscope and operational principles of confocal fluorescence microscopy.Methods Cell Biol. 1989; 31: 437-452
- Position and orientation of phalloidin in F-actin determined by X-ray fiber diffraction analysis.Biophys J. 2005; 88: 2727-2736
- The chemistry and mechanism of antibody binding to protein antigens.Adv Immunol. 1988; 43: 1-98
- Impact of immunization technology and assay application on antibody performance–a systematic comparative evaluation.PLoS One. 2011; 6: e28718
- Dissecting antibodies with regards to linear and conformational epitopes.PLoS One. 2015; 10: e0121673
- Nanobodies: natural single-domain antibodies.Annu Rev Biochem. 2013; 82: 775-797
- A novel protocol of whole mount electro-immunofluorescence staining.Mol Vis. 2009; 15: 505-517
- Spectral imaging: principles and applications.Cytometry A. 2006; 69: 735-747
- Frequency domain lifetime and spectral imaging microscopy.Microsc Res Tech. 2006; 69: 861-874
- Intravital microscopy of biosensor activities and intrinsic metabolic states.Methods. 2017; 128: 95-104
- Two-photon intravital fluorescence lifetime imaging of the kidney reveals cell-type specific metabolic signatures.J Am Soc Nephrol. 2017; 28: 2420-2430
- Phasor approach to fluorescence lifetime microscopy distinguishes different metabolic states of germ cells in a live tissue.Proc Natl Acad Sci U S A. 2011; 108: 13582-13587
- Rapid imaging of surgical breast excisions using direct temporal sampling two photon fluorescent lifetime imaging.Biomed Opt Express. 2015; 6: 4317-4325
- Memoir on inventing the confocal scanning microscope.Scanning. 1988; 10: 128-138
- Serial two-photon tomography for automated ex vivo mouse brain imaging.Nat Methods. 2012; 9: 255-258
- Whole brain imaging with serial two-photon tomography.Front Neuroanat. 2016; 10: 31
- ACT-presto: biological tissue clearing and Immunolabeling methods for volume imaging.J Vis Exp. 2016; 118
- Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.Cell. 2014; 157: 726-739
- A simple introduction to multiphoton microscopy.J Microsc. 2011; 243: 221-226
- Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain.Nat Neurosci. 2011; 14: 1481-1488
- Scalable and DiI-compatible optical clearance of the mammalian brain.Front Neuroanat. 2015; 9: 19
- Über Sichtbarmachung und Groessenbestimmung ultra mikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubinglaesern.Annalen der Physik. 1903; 10: 1-39
- Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain.Nat Methods. 2007; 4: 331-336
- Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens.J Microsc. 1993; 170: 229-236
- Light sheet fluorescence microscopy: a review.J Histochem Cytochem. 2011; 59: 129-138
- A guide to light-sheet fluorescence microscopy for multiscale imaging.Nat Methods. 2017; 14: 360-373
- Selective plane illumination microscopy techniques in developmental biology.Development. 2009; 136: 1963-1975
- Optical sectioning deep inside live embryos by selective plane illumination microscopy.Science. 2004; 305: 1007-1009
- Three-dimensional imaging of solvent-cleared organs using 3DISCO.Nat Protoc. 2012; 7: 1983-1995
- Optimization of CLARITY for clearing whole-brain and other intact Organs(1,2,3).eNeuro. 2015; 2: 1-15
- Multispectral fluorescence ultramicroscopy: three-dimensional visualization and automatic quantification of tumor morphology, drug penetration, and antiangiogenic treatment response.Neoplasia. 2014; 16: 1-13
- Extensible visualization and analysis for multidimensional images using Vaa3D.Nat Protoc. 2014; 9: 193-208
- Segmenting and tracking multiple dividing targets using ilastik.Adv Anat Embryol Cell Biol. 2016; 219: 199-229
- Fiji: an open-source platform for biological-image analysis.Nat Methods. 2012; 9: 676-682
- ClearVolume: open-source live 3D visualization for light-sheet microscopy.Nat Methods. 2015; 12: 480-481
- FluoRender: an application of 2D image space methods for 3D and 4D confocal microscopy data visualization in neurobiology research.IEEE Pac Vis Symp. 2012; : 201-208
- Voxx: a PC-based, near real-time volume rendering system for biological microscopy.Am J Physiol Cell Physiol. 2002; 282: C213-C218
- Microscopy-based multicolor tissue cytometry at the single-cell level.Cytometry A. 2004; 59: 182-190
- An improved method for discrimination of cell populations in tissue sections using microscopy-based multicolor tissue cytometry.Cytometry A. 2006; 69: 119-123
- Icy: an open bioimage informatics platform for extended reproducible research.Nat Methods. 2012; 9: 690-696
- Analysis of nuclear organization with TANGO, software for high-throughput quantitative analysis of 3D fluorescence microscopy images.Methods Mol Biol. 2015; 1228: 203-222
- TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.Bioinformatics. 2013; 29: 1840-1841
- Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.Nat Protoc. 2014; 9: 586-596
- BioImageXD: an open, general-purpose and high-throughput image-processing platform.Nat Methods. 2012; 9: 683-689
- Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes.Immunity. 2012; 37: 364-376
- Dynamic in situ cytometry uncovers T cell receptor signaling during immunological synapses and kinapses in vivo.Immunity. 2012; 37: 351-363
- Cell distance mapping identifies functional T follicular helper cells in inflamed human renal tissue.Sci Transl Med. 2014; 6: 230ra46
Article info
Publication history
Published online: July 21, 2017
Accepted:
July 18,
2017
Received in revised form:
June 26,
2017
Received:
April 1,
2017
Identification
Copyright
Published by Elsevier Inc.
