media:publications - diSPIM Wiki

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===== Publications =====

==== Microscopy-Focused ====

  * [[https://www.nature.com/articles/s41467-017-01250-8|Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy.]] Nat. Comm. 8:1452 (Nov 2017). doi: [[http://dx.doi.org/10.1038/s41467-017-01250-8|10.1038/s41467-017-01250-8]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/29129912|29129912]]
    * iSPIM/diSPIM on reflective substrate for 2/4 simultaneous views
  * [[https://www.nature.com/articles/nmeth.4224|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: [[http://www.ncbi.nlm.nih.gov/pubmed/28362435|28362435]]  
      * excellent review paper on light sheet microscopy in general
  * [[http://www.journals.uchicago.edu/doi/abs/10.1086/689589|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: [[http://dx.doi.org/10.1086/689589|10.1086/689589]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27638693|27638693]]
    * LabView implementation of both stage scanning and virtual slit on diSPIM
  * [[http://www.nature.com/articles/srep32880|πSPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes.]] Sci. Rep. 6:32880 (2016). doi: [[http://dx.doi.org/10.1038/srep32880|10.1038/srep32880]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27619647|27619647]]
    * independent invention/description of oSPIM concept developed by ASI (see {{:media:ascb_2016_ospim.pdf|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
  * [[https://www.osapublishing.org/optica/abstract.cfm?uri=optica-3-8-897|Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy.]] Optica 3(8):897-910 (2016). doi: [[http://dx.doi.org/10.1364/OPTICA.3.000897|10.1364/OPTICA.3.000897]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27761486 | 27761486]]
    * diSPIM with addition of capturing fluorescence from inverted microscope objective for improved resolution and light efficiency at cost of significantly increased complexity
  * [[http://www.nature.com/articles/srep23923|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: [[http://dx.doi.org/10.1038/srep23923|10.1038/srep23923]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27033347 | 27033347]]
    * homebuilt iSPIM with 2-photon excitation
  * [[http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3222.html|Guide to light-sheet microscopy for adventurous biologists]]. Nature Methods 12, 30–34 (2015). doi: [[http://dx.doi.org/10.1038/nmeth.3222|10.1038/nmeth.3222]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/25549268|25549268]]  [[https://publications.mpi-cbg.de/Reynaud_2015_6006.pdf|External link]].
      * overview and comparison of various SPIM techniques/microscopes, authored by OpenSPIM contributors
  * [[http://www.nature.com/nprot/journal/v9/n11/full/nprot.2014.172.html|Dual-view plane illumination microscopy for rapid and spatially isotropic imaging.]] Nat Protoc. 2014 Nov;9(11):2555-73. doi: [[http://dx.doi.org/10.1038/nprot.2014.172|10.1038/nprot.2014.172]]. PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/25299154|25299154]]
    * detailed protocol for diSPIM, some details different (and much easier) with more modern systems
  * [[http://www.nature.com/nbt/journal/v31/n11/full/nbt.2739.html|Two views on light sheets.]] Nat Biotechnol. 2013 Nov;31(11):992-3. doi: [[http://dx.doi.org/10.1038/nbt.2739|10.1038/nbt.2739]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/24213774|24213774]].  [[http://biologylabs.utah.edu/jorgensen/%20%20MANUSCRIPTS%20pdfs/2013%20Ebeling-light%20sheet%20microscopy%20%281%29.pdf|External link]].
      * overview of "Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy".
  * [[http://www.nature.com/nbt/journal/v31/n11/full/nbt.2713.html|Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy]].  Nat Biotechnol. 2013 Nov;31(11):1032-8. doi: [[http://dx.doi.org/10.1038/nbt.2713|10.1038/nbt.2713]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/24108093|24108093]].
  * [[http://www.pnas.org/content/108/43/17708|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: [[http://dx.doi.org/10.1073/pnas.1108494108|10.1073/pnas.1108494108]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/22006307|22006307]]
      * original single-sided implementation









==== Biology-Focused ====

  * [[https://www.nature.com/articles/s41586-020-03169-5|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
  * [[https://science.sciencemag.org/content/369/6499/71|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
  * [[https://jcs.biologists.org/content/133/11/jcs245043|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
  * [[https://www.nature.com/articles/s41598-020-66999-3|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
  * [[https://academic.oup.com/jmcb/advance-article/doi/10.1093/jmcb/mjz051/5512143 | 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 
  * [[https://www.biorxiv.org/content/10.1101/2020.04.11.037473v1|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)	
  * [[https://www.biorxiv.org/content/10.1101/525451v1.full|Multimodal cell type correspondence by intersectional mFISH in intact tissues]]. bioRxiv preprint doi: [[https://doi.org/10.1101/525451| 10.1101/525451]].
    * mFISH on iSPIM on cleared mouse brain using multi-immersion objective and Micro-Manager diSPIM plugin
  * [[http://www.bloodjournal.org/content/early/2018/11/06/blood-2018-08-867267| 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]]
  * [[https://www.tandfonline.com/doi/full/10.1080/09537104.2017.1420152| Mucor circinelloides induces platelet aggregation through integrin αIIbβ3 and FcγRIIA]]. Platelets. 2018 Jan 3:1-8. doi: [[https://doi.org/10.1080/09537104.2017.1420152|10.1080/09537104.2017.1420152]]  
  * [[http://www.cell.com/biophysj/fulltext/S0006-3495(17)30250-3|Visualizing Calcium Flux in Freely Moving Nematode Embryos]]. Biophysical Journal 112, 1975-1983 (2017). doi: [[http://dx.doi.org/10.1016/j.bpj.2017.02.035 | 10.1016/j.bpj.2017.02.035]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/28494967 | 28494967]]
    * functional imaging of calcium indicators to correlate neuronal and muscular activity on iSPIM
    * associated commentary by Phillip Keller at doi: [[http://dx.doi.org/10.1016/j.bpj.2017.03.035 | 10.1016/j.bpj.2017.03.035]]
  * [[http://www.molbiolcell.org/content/27/13/2000|Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium]]. Mol. Biol. of the Cell 27:13 2000-2007, (2016). doi: [[http://dx.doi.org/10.1091/mbc.E16-02-0129 |10.1091/mbc.E16-02-0129 ]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27193301 | 27193301]]
    * used diSPIM to track nuclei in Ashbya fungi
  * [[http://www.cell.com/biophysj/abstract/S0006-3495(16)30460-X|Snapshot Hyperspectral Light-Sheet Imaging of Signal Transduction in Live Pancreatic Islets]]. Biophysical Journal 111, 409-417 (2016). doi: [[http://dx.doi.org/10.1016/j.bpj.2016.06.014|10.1016/j.bpj.2016.06.014]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/27463142|27463142]]
    * combines iSPIM with hyperspectral imaging
  * [[https://elifesciences.org/content/4/e10070|Untwisting the Caenorhabditis elegans embryo]]. Nature Cell Biology 17, 397–408 (2015). doi: [[http://dx.doi.org/10.7554/eLife.10070|10.7554/eLife.10070]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/26633880| 26633880]]
    * obtained composite model showing average movement of neurons during development of worm embryos despite twitching
  * [[http://www.nature.com/ncb/journal/v17/n4/full/ncb3138.html|Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation]]. Nature Cell Biology 17, 397–408 (2015). doi: [[http://dx.doi.org/10.1038/ncb3138|10.1038/ncb3138]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/25812521 | 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
  * [[http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003971|Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm]]. PLoS Pathog. 2014 Mar 6;10(3):e1003971. doi: [[http://dx.doi.org/10.1371/journal.ppat.1003971|10.1371/journal.ppat.1003971]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/24603687|24603687 ]]
  * [[http://www.pnas.org/content/108/43/17708|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: [[http://dx.doi.org/10.1073/pnas.1108494108|10.1073/pnas.1108494108]].  PMID: [[http://www.ncbi.nlm.nih.gov/pubmed/22006307|22006307]]
==== Other ====

  * [[https://www.nature.com/articles/s42003-018-0079-6|Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours]]. Communications Biology Vol 1, Article number: 73 (2018); doi: [[https://doi.org/10.1038/s42003-018-0079-6| 10.1038/s42003-018-0079-6]].
    * convenient method of fixing e.g. nematode adults for diSPIM imaging
  * [[https://www.photonics.com/Articles/Light_Sheet_Microscopy_Transforming_3D/a65704|Light Sheet Microscopy: Transforming 3D Fluorescence Imaging]]. BioPhotonics May/Jun 2020.
    * semi-technical overview of light sheet microscopy for newcomers
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