Publications

Welcome to the arivis customer publication list, with articles and papers across all fields and disciplines.

Mihail Ivilinov Todorov, Johannes C. Paetzold, Oliver Schoppe, Giles Tetteh, Velizar Efremov, Katalin Völgyi, Marco Düring, Martin Dichgans, Marie Piraud, Bjoern Menze, Ali Ertürk


Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo

Saykali B, Mathiah N, Nahaboo W, Racu ML, Hammou L, Defrance M, Migeotte I. Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo. 

Elife. 2019 Apr 5;8:e42434.
doi: 10.7554/eLife.42434.
PubMed PMID: 30950395; PubMed Central PMCID: PMC6450669.

Methods: Time-lapse confocal microscopy
Product: arivis Vision4D - Image processing, Drift correction , Analysis and segmentation, Surface, volume, long/short axis ratio of 2D inner ellipse, and straightness were calculated by V4D


Oscillatory cortical forces promote three dimensional cell intercalations that shape the murine mandibular arch

Tao H, Zhu M, Lau K, Whitley OKW, Samani M, Xiao X, Chen XX, Hahn NA, Liu W, Valencia M, Wu M, Wang X, Fenelon KD, Pasiliao CC, Hu D, Wu J, Spring S, Ferguson J, Karuna EP, Henkelman RM, Dunn A, Huang H, Ho HH, Atit R, Goyal S, Sun Y, Hopyan S. Oscillatory cortical forces promote three dimensional cell intercalations that shape the murine mandibular arch. 

Nat Commun. 2019 Apr 12;10(1):1703.
doi: 10.1038/s41467-019-09540-z.
PubMed PMID: 30979871; PubMed Central PMCID: PMC6461694.

Methods: Multi-Photon confocal microscopy
Product: arivis Vision4D - Analysis and quantification


 

Targeted drug delivery via caveolae-associated protein PV1 improves lung fibrosis

Marchetti GM, Burwell TJ, Peterson NC, Cann JA, Hanna RN, Li Q, Ongstad EL, Boyd JT, Kennedy MA, Zhao W, Rickert KW, Grimsby JS, Dall'Acqua WF, Wu H, Tsui P, Borrok MJ, Gupta R. Targeted drug delivery via caveolae-associated protein PV1 improves lung fibrosis. 
Commun Biol. 2019 Mar 7;2:92.
doi: 10.1038/s42003-019-0337-2.
PubMed PMID: 30854484; PubMed Central PMCID: PMC6405929.

Methods: Live time-lapse light sheet microscopy
Product: arivis Vision4D - Analysis


Glucocorticoid receptor in astrocytes regulates midbrain dopamine neurodegeneration through connexin hemichannel activity

Maatouk L, Yi C, Carrillo-de Sauvage MA, Compagnion AC, Hunot S, Ezan P, Hirsch EC, Koulakoff A, Pfrieger FW, Tronche F, Leybaert L, Giaume C, Vyas S. Glucocorticoid receptor in astrocytes regulates midbrain dopamine neurodegeneration through connexin hemichannel activity. 
Cell Death Differ
. 2019 Mar;26(3):580-596.
doi: 10.1038/s41418-018-0150-3.
Epub 2018 Jul 13.
PubMed PMID: 30006609; PubMed Central PMCID: PMC6370798.

Methods: Confocal laser-scanning microscopy
Product: arivis Vision4D - 3d reconstruction


 

A SEPT1-based scaffold is required for Golgi integrity and function

Song K, Gras C, Capin G, Gimber N, Lehmann M, Mohd S, Puchkov D, Rödiger M, Wilhelmi I, Daumke O, Schmoranzer J, Schürmann A, Krauss M. A SEPT1-based scaffold is required for Golgi integrity and function. 
J Cell Sci. 2019 Feb 1;132(3):jcs225557.
doi: 10.1242/jcs.225557.
PubMed PMID: 30709970; PubMed Central PMCID: PMC6382012.

Methods: Structured-illumination microscopy
Product: arivis Vision4D - Analysis and Python scripting, 3D rendering


 

GATA3 Promotes the Neural Progenitor State but Not Neurogenesis in 3D Traumatic Injury Model of Primary Human Cortical Astrocytes

Celikkaya H, Cosacak MI, Papadimitriou C, Popova S, Bhattarai P, Biswas SN, Siddiqui T, Wistorf S, Nevado-Alcalde I, Naumann L, Mashkaryan V, Brandt K, Freudenberg U, Werner C, Kizil C. GATA3 Promotes the Neural Progenitor State but Not Neurogenesis in 3D Traumatic Injury Model of Primary Human Cortical Astrocytes. 

Front Cell Neurosci. 2019 Feb 11;13:23.
doi: 10.3389/fncel.2019.00023.
PubMed PMID: 30809125; PubMed Central PMCID: PMC6380212.

Methods: Cellular neuroscience, Fluorescence imaging
Product: arivis Vision4D - Analysis and quantification


Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections MORE

Ruiyao Cai, Chenchen Pan, Alireza Ghasemigharagoz, Mihail Ivilinov Todorov, Benjamin Förstera, Shan Zhao, Harsharan S. Bhatia, Arnaldo Parra-Damas, Leander Mrowka, Delphine Theodorou, Markus Rempfler, Anna L. R. Xavier, Benjamin T. Kress, Corinne Benakis, Hanno Steinke, Sabine Liebscher, Ingo Bechmann, Arthur Liesz, Bjoern Menze, Martin Kerschensteiner, Maiken Nedergaard & Ali Ertürk

Nature Neuroscience volume 22, pages 317–327 (2019)
Published: 31 December 2018
https://doi.org/10.1038/s41593-018-0301-3

Methods: Fluorescence imaging
Product: arivis Vision4D - 4D Viewer


Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution  MORE

BY RUIXUAN GAO, SHOH M. ASANO, SRIGOKUL UPADHYAYULA, IGOR PISAREV, DANIEL E. MILKIE, TSUNG-LI LIU, VED SINGH, AUSTIN GRAVES, GRACE H. HUYNH, YONGXIN ZHAO, JOHN BOGOVIC, JENNIFER COLONELL, CAROLYN M. OTT, CHRISTOPHER ZUGATES, SUSAN TAPPAN, ALFREDO RODRIGUEZ, KISHORE R. MOSALIGANTI, SHU-HSIEN SHEU, H. AMALIA PASOLLI, SONG PANG, C. SHAN XU, SEAN G. MEGASON, HARALD HESS, JENNIFER LIPPINCOTT-SCHWARTZ, ADAM HANTMAN, GERALD M. RUBIN, TOM KIRCHHAUSEN, STEPHAN SAALFELD, YOSHINORI ASO, EDWARD S. BOYDEN, ERIC BETZIG

Science  18 Jan 2019:
Vol. 363, Issue 6424, eaau8302
DOI: 10.1126/science.aau8302

Methods: Combined expansion and lattice light-sheet microscopy
Product: arivis Vision4D - 4D Viewer, 2D Viewer, visualization, drawing tools, Clipping on ROI, storyboard, movie export, 3D Masking, Analysis Pipeline


A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples

Kerstens, A., Corthout, N., Pavie, B., Huang, Z., Vernaillen, F., Vande Velde, G., & Munck, S. (2019).
BMC biology, 17(1), 1.
Published online 2019 Jan 7
doi:10.1186/s12915-018-0614-4

Methods: ALMOST-novel optical method for 3D surface imaging of reflective opaque objects utilizing an optical projection tomography device in combination with oblique illumination and optical filters
Product: arivis Vision4D - 4D Viewer: 3D Visualization; Maximum intensity projection combining all colors in arivis 3D rendering software


Optical Clearing in the Kidney Reveals Potassium-Mediated Tubule Remodeling

Turgay Saritas, Victor G. Puelles, Xiao-Tong Su, James A. McCormick, Paul A. Welling, David H. Ellison
Cell Reports VOLUME 25, ISSUE 10, P2668-2675.E3, DECEMBER 04, 2018
DOI:https://doi.org/10.1016/j.celrep.2018.11.021

Methods: Optical kidney clearing, Clarity,  confocal microscopy, light-sheet microscopy
Product: arivis Vision4D - 4D Viewer: 3D Rendering of PI+ nuclei, AQP2+and pThr53-NCC+ tubules


Non-Muscle Myosin II Drives Vesicle Loss During Human Reticulocyte Maturation

Pedro L. Moura, Bethan R. Hawley, Tosti J. Mankelow, Rebecca E. Griffiths, Johannes G.G. Dobbe, Geert J. Streekstra, David J. Anstee, Timothy J.Satchwell, Ashley M. Toye
Published By Haematologica
Print ISSN 0390-6078
Online ISSN 1592-8721
Haematologica Dec 2018, 103 (12) 1997-2007
DOI: 10.3324/haematol.2018.199083

Methods: Confocal microscopy
Product: arivis Vision4D - 4D Viewer3D reconstruction, data visualization, Analysis: Manually quantification of cells stained with PDI antibody; Special: protocol which facilitates algorithm-based segmentation in large planes created from individual image stitching


Cortical bone is an extraneuronal site of norepinephrine uptake in adult mice

Zhu, Y., Ma, Y., & Elefteriou, F. (2018)
Bone reports, 9, Dec 2018, 188-198.
doi:10.1016/j.bonr.2018.11.002

Methods: Whole mount light sheet microscopy, CLARITY
Product: arivis Vision4D - Tile Sorter, tiff-export


Macropinosome formation by tent pole ruffling in macrophages

Nicholas D. Condon, John M. Heddleston, Teng-Leong Chew, Lin Luo, Peter S. McPherson, Maria S. Ioannou, Louis Hodgson, Jennifer L. Stow, Adam A. Wall
J Cell Biol Nov 2018, 217 (11) 3873-3885; 
DOI: 10.1083/jcb.201804137

Methods: Lattice light sheet microscopy
Product: arivis Vision4D - 4D Viewer for 3D Volume rendering


Endogenous Ovarian Angiogenesis in Polycystic Ovary Syndrome-Like Rats Induced by Low-Frequency Electro-Acupuncture: The CLARITY Three-Dimensional Approach

Ma, Tong; Cui, Peng; Tong, Xiaoyu; Hu, Wei; Shao, Linus R.; Zhang, Feifei; Li, Xin; Feng, Yi. 2018.
Int. J. Mol. Sci. 19, no. 11: 3500.
Published: 7 November 2018
doi: 10.3390/ijms19113500

Methods: Light-sheet fluorescence microscopy, CLARITY
Product: arivis Vision4D - data compression, tiff-export


Experimental Traumatic Brain Injury Identifies Distinct Early and Late Phase Axonal Conduction Deficits of White Matter Pathophysiology, and Reveals Intervening Recovery

Christina M. Marion, Kryslaine L. Radomski, Nathan P. Cramer, Zygmunt Galdzicki, Regina C. Armstrong
PubMed 30143572
Published By Society for Neuroscience
Published in print October 10, 2018
Journal of Neuroscience 10 October 2018, 38 (41) 8723-8736
DOI https://doi.org/10.1523/JNEUROSCI.0819-18.2018
Methods: Confocal microscopy, CLARITY
Product: arivis Vision4D - 4D Viewer3D reconstruction, data visualization, image-to-image filter (curvature flow), image rotation, fly-through, and varying channel visibility levels


3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method

Liang, H., Wang, H., Wang, S., Francis, R., Paxinos, G., & Huang, X. (2018). 
Molecular Brain 2018, 11:50.
Published: 12 September 2018
doi:10.1186/s13041-018-0393-4

Methods: Light-sheet fluorescence microscopy, CUBIC
Product: arivis Vision4D - 4D Viewer3D reconstruction, data visualization and high resolution screenshots


The effects of mechanical strain on mouse eye lens capsule and cellular microstructure

Parreno, J., Cheng, C., Nowak, R. B., & Fowler, V. M. (2018)
Molecular biology of the cell, Aug 8; 29(16).29(16), 1963-1974.
doi: 10.1091/mbc.E18-01-0035

Methods: Laser-scanning confocal microscopy
Product: arivis Vision4D - 4D Viewer3D reconstruction


Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice

Ruiyao Cai, Chenchen Pan, Alireza Ghasemigharagoz, Mihail I. Todorov, Benjamin Foerstera, Shan Zhao, Harsharan S. Bhatia, Leander Mrowka, Delphine Theodorou, Markus Rempfler, Anna Xavier, Benjamin T. Kress, Corinne Benakis, Arthur Liesz, Bjoern Menze, Martin Kerschensteiner, Maiken Nedergaard, Ali Ertürk
Nature 563, 305-306 (2018)
Preprint on BioRxiv, July 23, 2018
doi: 10.1038/d41586-018-07336-7

Methods: Light-sheet fluorescence microscopy, vDISCO
Product: arivis Vision4D - Tile Sorter: Alignment & Stitching; Scope Fusion, 4D Viewer3-D rendering (volumetric rendering), data visualization and movie export


Fundamental parameters of the developing thymic epithelium in the mouse

Hirakawa M, Nagakubo D, Kanzler B, Avilov S, Krauth B, Happe C, Swann JB, Nusser A, Boehm T. Fundamental parameters of the developing thymic epithelium in the mouse. 
Sci Rep. 2018 Jul 23;8(1):11095.
doi: 10.1038/s41598-018-29460-0.
PubMed PMID: 30038304; PubMed Central PMCID: PMC6056470.

Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - Tile Sorter: Alignment & Stitching


Dual-spindle formation in zygotes keeps parental genomes apart in early mammalian embryos

Judith Reichmann, Bianca Nijmeijer, M. Julius Hossain, Manuel Eguren, Isabell Schneider, Antonio Z. Politi, M. Julia Roberti, Lars Hufnagel, Takashi Hiiragi, Jan Ellenberg,
Science 13 Jul 2018:
Vol. 361, Issue 6398, pp. 189-193
DOI: 10.1126/science.aar7462

Methods: Light-sheet fluorescence microscopy
Product: arivis Vision4D - 4D Viewer: MIP Rendering and Time-lapse movie export Analysis: Filter, Segmentation, Tracking


Dual leucine zipper kinase is required for mechanical allodynia and microgliosis after nerve injury

Wlaschin, J. J., Gluski, J. M., Nguyen, E., Silberberg, H., Thompson, J. H., Chesler, A. T., & Le Pichon, C. E. (2018). Dual leucine zipper kinase is required for mechanical allodynia and microgliosis after nerve injury. 
eLife
7, e33910
http://doi.org/10.7554/eLife.33910

Methods: volumetric imaging of immunostained whole organs (iDISCO), Lightsheet Microscopy, 2-Photon Microscopy, Confocal Microscopy
Product: arivis Vision4D - 4D Viewer: 3-D rendering (volumetric rendering), visualization, movie generation, Analysis: Segmentation


NMDA-receptor inhibition and oxidative stress during hippocampal maturation differentially alter parvalbumin expression and gamma-band activity

Hasam-Henderson, L. A., Gotti, G. C., Mishto, M., Klisch, C., Gerevich, Z., Geiger, J. R. P., & Kovács, R. (2018). NMDA-receptor inhibition and oxidative stress during hippocampal maturation differentially alter parvalbumin expression and gamma-band activity. 
Scientific Reports8, 9545.
http://doi.org/10.1038/s41598-018-27830-2

Methods: spinning disk confocal microscope, multiphoton microscopy
Product: arivis Vision4D - 4D Viewer: 3-D reconstruction of the complete hippocampal slice, visualization; Analysis: quantification of the number of YFP+ (and PV+) interneurons with the BlobFinder operator


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


A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES. A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. 
Nat Chem Biol. 2018 Apr;14(4):352-360.
doi: 10.1038/s41589-018-0004-9. Epub 2018 Feb 26.
Erratum in: Nat Chem Biol. 2018 Mar 8;:. PubMed PMID: 29483642; PubMed Central PMCID: PMC5866759.

Methods: Light-sheet microscopy
Product: arivis Vision4D - Tile Sorter: Alignment & Stitching


Inter-chromosomal contact properties in live-cell imaging and in Hi-C

Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. 
Mol Cell
. 2018 Mar 15;69(6):1039-1045.e3.
doi: 10.1016/j.molcel.2018.02.007. Epub 2018 Mar 8.
Erratum in: Mol Cell. 2018 Apr 5;70(1):188-189. PubMed PMID: 29526697; PubMed Central PMCID: PMC5856634.

Methods: Confocal super-resolution microscopy
Product: arivis Vision4D- Analysis, Cropping


 

 

Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING)

Maass, P. G., Barutcu, A. R., Shechner, D. M., Weiner, C. L., Melé, M., & Rinn, J. L. (2018) 
Nature structural & molecular biology, 25(2), 176-184.
PMCID: PMC5805655
Published online 2018 Jan 8
doi: 10.1038/s41594-017-0015-3
Methods: confocal super- resolution microscopy; CRISPR live-cell imaging
Product: arivis Vision4D - 4D Viewer:


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


MyMiCROscope—Intelligent virtual microscopy in a blended learning model at Ulm University

C.Schmidt, M.Reinehr, O.Leucht, N.Behrendt, S.Geiler, S.Britsch
Publication: Annals of Anatomy - Anatomischer Anzeiger
Publisher: Elsevier
Date: 20 October 2011
Applications: E-Learning; Microscopic anatomy
Product: arivis Webview