media:publications

Publications

Publications

Microscopy-Focused

Airy light-sheet Raman imaging. Optics Express 29, 31941-31951 (2021). doi: 10.1364/OE.435293. PMID: 34615275
- used ASI scanner and custom ASI XYZ stage on inverted microscope
Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy. Nat. Comm. 8:1452 (Nov 2017). doi: 10.1038/s41467-017-01250-8. PMID: 29129912
- iSPIM/diSPIM on reflective substrate for 2/4 simultaneous views
A guide to light-sheet fluorescence microscopy for multiscale imaging. Nature Methods 14, 360–373 (2017). doi: http://dx.doi.org/10.1038/nmeth.4224. PMID: 28362435
- excellent review paper on light sheet microscopy in general
Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM). Biol. Bull. 231:26-39 (Aug 2016). doi: 10.1086/689589. PMID: 27638693
- LabView implementation of both stage scanning and virtual slit on diSPIM
πSPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes. Sci. Rep. 6:32880 (2016). doi: 10.1038/srep32880. PMID: 27619647
- independent invention/description of oSPIM concept developed by ASI (see ASI Oblique SPIM Dec 2016)
- take resolution numbers with a grain of salt, authors use large illumination NA (very short beam waist) to get excellent optical sectioning but with impractically narrow field of view
Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy. Optica 3(8):897-910 (2016). doi: 10.1364/OPTICA.3.000897. PMID: 27761486
- diSPIM with addition of capturing fluorescence from inverted microscope objective for improved resolution and light efficiency at cost of significantly increased complexity
4D (x-y-z-t) imaging of thick biological samples by means of Two-Photon inverted Selective Plane Illumination Microscopy (2PE-iSPIM) Sci. Rep. 6:23923 (2016). doi: 10.1038/srep23923. PMID: 27033347
- homebuilt iSPIM with 2-photon excitation
Guide to light-sheet microscopy for adventurous biologists. Nature Methods 12, 30–34 (2015). doi: 10.1038/nmeth.3222. PMID: 25549268 External link.
- overview and comparison of various SPIM techniques/microscopes, authored by OpenSPIM contributors
Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nat Protoc. 2014 Nov;9(11):2555-73. doi: 10.1038/nprot.2014.172. PMID: 25299154
- detailed protocol for diSPIM, some details different (and much easier) with more modern systems
Two views on light sheets. Nat Biotechnol. 2013 Nov;31(11):992-3. doi: 10.1038/nbt.2739. PMID: 24213774. External link.
- overview of “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy”.
Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol. 2013 Nov;31(11):1032-8. doi: 10.1038/nbt.2713. PMID: 24108093.
Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17708-13. doi: 10.1073/pnas.1108494108. PMID: 22006307
- original single-sided implementation

Biology-Focused

Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system. Cell Research 2024. doi: https://doi.org/10.1038/s41422-023-00867-3.
Efficient 3D light-sheet imaging of very large-scale optically cleared human brain and prostate tissue samples. Comm. Biology 2023. doi: https://doi.org/10.1038/s42003-023-04536-4.
Using light-sheet microscopy to study spontaneous activity in the developing lateral-line system. bioRxiv 2021. doi: https://doi.org/10.1101/2021.11.23.469686.
Structural and developmental principles of neuropil assembly in C. elegans. Nature, 591, 99–104 (2021). doi: https://doi.org/10.1038/s41586-020-03169-5.
- Neural development tracked by diSPIM in worm embryos
Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy. Science, 369, 71-77 (2020). doi: https://doi.org/10.1126/science.abb8501.
- biofilm development tracked by diSPIM
Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes. J. Cell Sci, 133 (2020). doi: https://doi.org/ 10.1242/jcs.245043.
- adapted diSPIM toward high-throughput screening applications for cell cycle studies
hFRUIT: An optimized agent for optical clearing of DiI-stained adult human brain tissue. Sci Rep 10, 9950 (2020). doi: https://doi.org/10.1038/s41598-020-66999-3.
- clearing protocol for human brain tissue and imaging on ct-dSPIM with 54-10-12 objectives
Mitotic motor CENP-E cooperates with PRC1 in temporal control of central spindle assembly Journal of Molecular Cell Biology, mjz051, 10 September 2019 https://doi.org/10.1093/jmcb/mjz051
- diSPIM on a 3i - Marianas Platform (Marianas LightSheet), software SlideBook
Multiscale three-dimensional pathology findings of COVID-19 diseased lung using high-resolution cleared tissue microscopy. bioRxiv preprint doi: https://doi.org/10.1101/2020.04.11.037473.
- iSPIM imaging of cleared lung tissue using cleared tissue objective (software unspecified)
Multimodal cell type correspondence by intersectional mFISH in intact tissues. bioRxiv preprint doi: 10.1101/525451.
- mFISH on iSPIM on cleared mouse brain using multi-immersion objective and Micro-Manager diSPIM plugin
Salmonella-induced thrombi in mice develop asynchronously in the spleen and liver and are not effective bacterial traps. Blood. 2018 Nov 6. https://doi.org/10.1182/blood-2018-08-867267
Mucor circinelloides induces platelet aggregation through integrin αIIbβ3 and FcγRIIA. Platelets. 2018 Jan 3:1-8. doi: 10.1080/09537104.2017.1420152
Visualizing Calcium Flux in Freely Moving Nematode Embryos. Biophysical Journal 112, 1975-1983 (2017). doi: 10.1016/j.bpj.2017.02.035. PMID: 28494967
- functional imaging of calcium indicators to correlate neuronal and muscular activity on iSPIM
- associated commentary by Phillip Keller at doi: 10.1016/j.bpj.2017.03.035
Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium. Mol. Biol. of the Cell 27:13 2000-2007, (2016). doi: 10.1091/mbc.E16-02-0129 . PMID: 27193301
- used diSPIM to track nuclei in Ashbya fungi
Snapshot Hyperspectral Light-Sheet Imaging of Signal Transduction in Live Pancreatic Islets. Biophysical Journal 111, 409-417 (2016). doi: 10.1016/j.bpj.2016.06.014. PMID: 27463142
- combines iSPIM with hyperspectral imaging
Untwisting the Caenorhabditis elegans embryo. Nature Cell Biology 17, 397–408 (2015). doi: 10.7554/eLife.10070. PMID: 26633880
- obtained composite model showing average movement of neurons during development of worm embryos despite twitching
Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation. Nature Cell Biology 17, 397–408 (2015). doi: 10.1038/ncb3138. PMID: 25812521
- uses a homebuilt instrument that is essentially an iSPIM with Nikon 10x/0.3 objectives and no inverted microscope to study chick embryo development
Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm. PLoS Pathog. 2014 Mar 6;10(3):e1003971. doi: 10.1371/journal.ppat.1003971. PMID: 24603687
Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17708-13. doi: 10.1073/pnas.1108494108. PMID: 22006307

Other

Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours. Communications Biology Vol 1, Article number: 73 (2018); doi: 10.1038/s42003-018-0079-6.
- convenient method of fixing e.g. nematode adults for diSPIM imaging
Light Sheet Microscopy: Transforming 3D Fluorescence Imaging. BioPhotonics May/Jun 2020.
- semi-technical overview of light sheet microscopy for newcomers

Table of Contents

Publications

Microscopy-Focused

Biology-Focused

Other