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--- media:publications [2020/04/29 10:37]
Hella Baumann [Biology-Focused]
+++ media:publications [2024/05/17 00:05] (current)
Jon Daniels [Biology-Focused]
@@ Line 3: / Line 3: @@
 ==== Microscopy-Focused ====
+  * [[https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-29-20-31941&id=459719|Airy light-sheet Raman imaging.]] Optics Express 29, 31941-31951 (2021). doi: [[https://doi.org/10.1364/OE.435293|10.1364/OE.435293]]. PMID: [[https://pubmed.ncbi.nlm.nih.gov/34615275/|34615275]]
+      * used ASI scanner and custom ASI XYZ stage on inverted microscope
   * [[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
@@ Line 14: / Line 18: @@
   * [[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
@@ Line 21: / Line 27: @@
   * [[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
-  * [[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
-  * [[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]]
-      * overall excellent review paper
 ==== Biology-Focused ====
+  * [[https://www.nature.com/articles/s41422-023-00867-3|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]].
+  * [[https://www.nature.com/articles/s42003-023-04536-4|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]].
+  * [[https://www.biorxiv.org/content/10.1101/2021.11.23.469686v1|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]].
+  * [[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
@@ Line 39: / Line 69: @@
   * [[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]]
-  * [[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.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.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
-  * [[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://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
 ==== 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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