Publications

Welcome to the arivis Customer Publication list, with articles and papers across all fields and disciplines.

Abnormal neurogenesis and cortical growth in congenital heart disease

Morton, P. D., Korotcova, L., Lewis, B. K., Bhuvanendran, S., Ramachandra, S. D., Zurakowski, D., … Ishibashi, N. (2017). Abnormal neurogenesis and cortical growth in congenital heart disease. 
Science Translational Medicine9(374), eaah7029.
http://doi.org/10.1126/scitranslmed.aah7029
Methods:  three-dimensional imaging of solvent-cleared organs (iDISCO) data
Product: arivis Vision4D - 4D Viewer: 3-D rendering (volumetric rendering), visualization, Analysis: Segmentation


Spatial and temporal changes in extracellular elastin and laminin distribution during lung alveolar development

Luo, Y., Li, N., Chen, H., Fernandez, G. E., Warburton, D., Moats, R., … Shi, W. (2018). Spatial and temporal changes in extracellular elastin and laminin distribution during lung alveolar development.
Scientific Reports, 8, 8334.
http://doi.org/10.1038/s41598-018-26673-1
Methods:  Confocal microscopy
Product: arivis Vision4D - 4D Viewer: 3-D rendering (volumetric rendering), visualization, Analysis: Segmentation, and morphological analysis


Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions

Janes G, von Wangenheim D, Cowling S, et al. Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions. 
Frontiers in Plant Science
. 2018;9:735.
doi:10.3389/fpls.2018.00735
Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - 4D Viewer: 3D reconstruction and visualization


Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

Tsung-Li Liu, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, Tom W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N. Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L. Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig
Science  20 Apr 2018:
Vol. 360, Issue 6386, eaaq1392
DOI: 10.1126/science.aaq1392​
Methods: noninvasive lattice light-sheet microscopy combined with aberration-correcting adaptive optics
Product: arivis Vision4D - 4D Viewer: Rendering and Movie export 


 

Plasma membrane LAT activation precedes vesicular recruitment defining two phases of early T-cell activation

Lakshmi Balagopalan, Jason Yi, Tiffany Nguyen, Katherine M. McIntire, Adam S. Harned, Kedar Narayan & Lawrence E. Samelson
Nat Communication 9, 2018, May 22
doi:10.1038/s41467-018-04419-x
Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - 4D Viewer: Rendering and Movie export Analysis: Filter, Segmentation, Tracking

"Vision4D (Arivis) was used for tracking of VAMP7 vesicles and colocalization of analysis of VAMP7 vesicles with microclusters from TIRF-SIM data (Fig. 5b). Data were filtered, segmented, and tracked as follows. We first applied a type of image-restoration filter (called 2D particle enhancement in Vision4D) that enhances detection of feature points in frame images (time series) that greatly reduced the detection of questionable positive signals coming from background and enriched for true signals coming from objects (our observation). For each frame series, we then inspected the images and iteratively evaluated intensity-threshold values to find the most reliable segmentation of vesicles and microclusters into objects. A segment generator was used to convert the signals above the threshold into objects. The Vision4D software provides an object-based colocalization operation that tags objects when they meet user-defined criteria. In this case, we set the operation so that when a vesicle touches a microcluster, it is tagged as being colocalized with the microcluster. This operation was performed on all frames of each time series. The movement of the objects over time was then tracked with a segment-tracking operation and all the results transferred to a spreadsheet for quantitation."


Whole Organ Blood and Lymphatic Vessels Imaging (WOBLI)

Oren, R., Fellus-Alyagor, L., Addadi, Y., Bochner, F., Gutman, H., Blumenreich, S., … Lazar, S. (2018). Whole Organ Blood and Lymphatic Vessels Imaging (WOBLI). 
Scientific Reports8, 1412.
http://doi.org/10.1038/s41598-018-19663-w
Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - Tile Sorter: Alignment & Stitching; arivis Vision4D - 4D Viewer: 3D Visualization and projections


 

Disruption of dual zygotic spindle assembly shows epigenetic asymmetry to be chromosome intrinsic 

Judith Reichmann, Bianca Nijmeijer, M. Julius Hossain, Manuel Eguren, Isabell Schneider, Antonio Z. Politi, M. Julia Roberti, Lars Hufnagel, Takashi Hiiragi, Jan Ellenberg
bioRxiv preprint first posted online Oct. 4, 2017 
doi: https://doi.org/10.1101/198275
Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - 4D Viewer: MIP Rendering and Time-lapse movie export Analysis: Filter, Segmentation, Tracking


 

Mps1 kinase-dependent Sgo2 centromere localisation mediates cohesin protection in mouse oocyte meiosis I

Warif El Yakoubi, Eulalie Buffin, Damien Cladière, Yulia Gryaznova, Inés Berenguer, Sandra A. Touati, Rocío Gómez, José A. Suja, Jan M. van Deursen & Katja Wassmann
Nat Commun. 2017 Sep 25;8(1):694
doi: http://dx.doi.org/10.1038/s41467-017-00774-3
Applications & Methods: Confocal Microscopy
Product: arivis Vision4D - 4D Viewer: 3D Visualization


 

Antagonistic Activities of Sox2 and Brachyury Control the Fate Choice of Neuro-Mesodermal Progenitors

Frederic Koch, Manuela Scholze, Lars Wittler, Dennis Schifferl, Smita Sudheer, Phillip Grote, Bernd Timmermann, Karol Macura, Bernhard G. Herrmann
Developmental Cell, Volume 42, Issue 5, p514–526.e7, 11 September 2017 
doi: http://dx.doi.org/10.1016/j.devcel.2017.07.021
Application: Neurobiology, Developmental Biology Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - Image processing


 

A radial axis defined by semaphorin-to-neuropilin signaling controls pancreatic islet morphogenesis

Philip T. Pauerstein, Krissie Tellez, Kirk B. Willmarth, Keon Min Park, Brian Hsueh, H. Efsun Arda, Xueying Gu, Haig Aghajanian, Karl Deisseroth, Jonathan A. Epstein, Seung K. Kim
Development 2017 144: 3744-3754
doi: https://doi.org/10.1242/dev.148684
Methods: Clarity, Light-sheet fluorescence microscopy
Productarivis Vision4D - 4D Viewer: 3D reconstruction and movie


 

A new holistic 3D non-invasive analysis of cellular distribution and motility on fibroin-alginate microcarriers using light sheet fluorescent microscopy

Duchi S, Piccinini F, Pierini M, et al. A new holistic 3D non-invasive analysis of cellular distribution and motility on fibroin-alginate microcarriers using light sheet fluorescent microscopy.
Lai J-Y, ed. PLoS ONE. 2017;12(8):e0183336, Published online 2017 Aug 17
doi: https://doi.org/10.1371/journal.pone.0183336
Methods: Light-sheet fluorescence microscopy
Productarivis Vision4D - 4D Viewer: Reconstruction into a single 3D dataset


 

Functional Differentiation of Cholecystokinin-Containing Interneurons Destined for the Cerebral Cortex

Daniela Calvigioni, Zoltán Máté, János Fuzik, Fatima Girach, Ming-Dong Zhang, Andrea Varro, Johannes Beiersdorf, Christian Schwindling, Yuchio Yanagawa, Graham J. Dockray, Chris J. McBain, Tomas Hökfelt, Gábor Szabó, Erik Keimpema, Tibor Harkany;
Cerebral Cortex, Volume 27, Issue 4, 1 April 2017, Pages 2453–2468,
doi: https://doi.org/10.1093/cercor/bhw094

Applications: Neuroscience, cell migration 
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - 4D Viewer: 3D Visualization and High Resolution Rendering


 

Altered Protein Interactions of the Endogenous Interactome of PTPIP51 towards MAPK Signaling

Brobeil A, Chehab R, Dietel E, Gattenlöhner S, Wimmer M.
ed. Biomolecules. 2017;7(3):55.
doi:  https://doi.org/10.3390/biom7030055
Methods: Confocal Laser Scanning Microscopy
Productarivis Vision4D - 4D Viewer: 3D reconstruction


 

Chrna2-Martinotti Cells Synchronize Layer 5 Type A Pyramidal Cells via Rebound Excitation

Hilscher MM, Leão RN, Edwards SJ, Leão KE, Kullander K (2017)
PLoS Biol 15(2): e2001392
doi: https://doi.org/10.1371/journal.pbio.2001392
Applications: Neuroscience, Optogenetics Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - Tile Sorter: Alignment & Stitching


 

3D Visualization of Developmental Toxicity of 2,4,6-Trinitrotoluene in Zebrafish Embryogenesis Using Light-Sheet Microscopy

Eum, J.; Kwak, J.; Kim, H.J.; Ki, S.; Lee, K.; Raslan, A.A.; Park, O.K.; Chowdhury, M.A.U.; Her, S.; Kee, Y.; Kwon, S.-H.; Hwang, B.J. 
Int. J. Mol. Sci. 201617, 1925.
doi: https://doi.org/10.3390/ijms17111925
Methods: Light-sheet fluorescence microscopy
Productarivis Vision4D - 4D Viewer: 3D reconstruction


 

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes

Nicolas Renier, Eliza L. Adams, Christoph Kirst, Zhuhao Wu, Ricardo Azevedo, Johannes Kohl, Anita E. Autry, Lolahon Kadiri, Kannan Umadevi Venkataraju, Yu Zhou, Victoria X. Wang, Cheuk Y. Tang, Olav Olsen, Catherine Dulac, Pavel Osten, Marc Tessier-Lavigne
Cell, Volume 165, Issue 7, 16 June 2016, Pages 1789-1802
doi: http://dx.doi.org/10.1016/j.cell.2016.05.007
Applications: Neuroscience: Whole Brain Imaging Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - Tile Sorter: Alignment & Stitching


 

Distinct Neural Circuits for the Formation and Retrieval of Episodic Memories

Dheeraj S. Roy, Takashi Kitamura, Teruhiro Okuyama, Sachie K. Ogawa, Chen Sun, Yuichi Obata, Atsushi Yoshiki, Susumu Tonegawa
Cell, Volume 170, Issue 5, 24 August 2017, Pages 1000–1012.e19
doi: https://doi.org/10.1016/j.cell.2017.07.013
Applications: Neuroscience: Whole Brain Imaging, fluorescence Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - Tile Sorter: Alignment & Stitching - 4D Viewer: High Resolution Rendering


 

Neural Crest Cell Implantation Restores Enteric Nervous System Function and Alters the Gastrointestinal Transcriptome in Human Tissue-Engineered Small Intestine

Christopher R. Schlieve, Kathryn L. Fowler, Matthew Thornton, Sha Huang, Ibrahim Hajjali, Xiaogang Hou, Brendan Grubbs, Jason R. Spence and Tracy C. Grikscheit
Stem Cell Reports, Volume 9, Issue 3, 12 September 2017, Pages 883-896
doi: http://dx.doi.org/10.1016/j.stemcr.2017.07.017
Applications: Neuroscience: 3D spheroids 
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - Image processing


 

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Alexander Schmitz, Sabine C. Fischer, Christian Mattheyer, Francesco Pampaloni & Ernst H. K. Stelzer
Sci Rep. 2017 Mar 3;7:43693.
doi: https://dx.doi.org/10.1038/srep43693
Applications: Cell biology: 3D cell culture, image processing Methods: Optical clearing techniques, Light-sheet fluorescence microscopy
Productarivis Vision4D - 4D Viewer: 3D reconstruction


 

Parvalbumin- and vasoactive intestinal polypeptide-expressing neocortical interneurons impose differential inhibition on Martinotti cells

Walker, F. et al.
Nat. Commun. 7:13664
doi: https://dx.doi.org/10.1038/ncomms13664 (2016)
Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex Methods: Confocal microscopy
Product: arivis Vision4D - Tile Sorter: Stitch multiple, predefined tiles


 

Rules and Self-Organizing Properties of Post-embryonic Plant Organ Cell Division Patterns

Daniel von Wangenheim, Jens Fangerau, Alexander Schmitz, Richard S. Smith, Heike Leitte, Ernst H.K. Stelzer, Alexis Maizel

Current Biology , Volume 26 , Issue 4 , 439 - 449 (2016)
doi: https://dx.doi.org/10.1016/j.cub.2015.12.047
Published in: Current Biology
Applications: Plant cell and developmental biology: Development of Arabidopsis thaliana's root system Methods: Light-sheet based fluorescence microscopy
Product: arivis Vision4D 4D Viewer: 3D reconstruction, create and export movies


 

ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging

Eunsoo Lee, Jungyoon Choi, Youhwa Jo, Joo Yeon Kim, Yu Jin Jang, Hye Myeong Lee, So Yeun Kim, Ho-Jae Lee, Keunchang Cho, Neoncheol Jung, Eun Mi Hur, Sung Jin Jeong, Cheil Moon, Youngshik Choe, Im Joo Rhyu, Hyun Kim & Woong Sun
Scientific Reports 6, Article number: 18631 (2016)
doi: https://dx.doi.org/10.1038/srep18631
Published in: nature.com
Applications: Neuroscience: Whole BraIn Imaging Methods: Optical imaging, fluorescence imaging, optical clearing techniques, light-sheet fluorescence microscopy
Product: arivis Vision4D 4D Viewer: Create and export movies - Tile Sorter: Aligning of whole-mouse brain and spinal cord images into large image stacks


 

Thalamocortical Connections Drive Intracortical Activation of Functional Columns in the Mislaminated Reeler Somatosensory Cortex

Robin J. Wagener, Mirko Witte, Julien Guy, Nieves Mingo-Moreno, Sebastian Kügler and Jochen F. Staiger

Cereb. Cortex (2016) 26 (2): 820-837 
doi:  https://dx.doi.org/10.1093/cercor/bhv257
Published in: Cerebral Cortex Oxford Journal
Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex Methods: Confocal microscopy
Product: arivis Vision4D - Tile Sorter: Stitch multiple, predefined tiles


 

The disorganized visual cortex in reelin-deficient mice is functional and allows for enhanced plasticity

Justyna Pielecka-Fortuna, corresponding author Robin Jan Wagener, Ann-Kristin Martens, Bianka Goetze, Karl-Friedrich Schmidt, Jochen F. Staiger, corresponding author and Siegrid Löwel

Brain Struct & Funct. 2015; 220(6): 3449–3467
​doi:  https://dx.doi.org/10.1007/s00429-014-0866-x
Published in: Springer: Brain Structure and Function
Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex Methods: Confocal microscopy
Product: arivis Vision4D - Tile Sorter: Stitch multiple, predefined tiles


 

Contour based Split and Merge Segmentation and Pre-classification of Zooplankton in Very Large Images

Enrico Gutzeit , Christian Scheel , Tim Dolereit and Matthias Rust
Published in: Computer Vision Theory and Applications (VISAPP), 2014 International Conference on  (Volume:1 )
Publisher: IEEE
Applications: Zooplankton Methods: Inverted light microscopy
Product: arivis Vision4D - Tile Sorter: Automated stitching to create a large plane from the single tiles