Publications

Welcome to the arivis Customer Publication List, with articels and papers across all fields and disciplines.

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 ​ 

Applications & Methods

Methods: Light-sheet fluorescence microscopy

4D Viewer: MIP Rendering and Time-lapse movie export

Analysis: Segmentation

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

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 

Applications & Methods
Neurobiology, Developmental Biology
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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

Applications & Methods

Methods: Clarity, Light-sheet fluorescence microscopy

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

Applications & Methods

Methods: Light-sheet fluorescence microscopy

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 & Methods
Neuroscience, cell migration
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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

Applications & Methods

Methods: Confocal Laser Scanning Microscopy

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 & Methods
Neuroscience, Optogenetics
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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

Applications & Methods

Methods: Light-sheet fluorescence microscopy

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 & Methods
Neuroscience: Whole Brain Imaging
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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 & Methods
Neuroscience: Whole Brain Imaging, fluorescence
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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 & Methods
Neuroscience: 3D spheroids
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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 & Methods
Cell biology: 3D cell culture, image processing
Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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 & Methods
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 & Methods
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 & Methods
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 & Methods
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 & Methods
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 & Methods
Zooplankton
Methods: Inverted light microscopy
Product
arivis Vision4D
Tile SorterAutomated stitching to create a large plane from the single tiles