Welcome to the arivis customer publication list, with articles and papers across all fields and disciplines.
Below you can find publications that utilize our technology.
Below you can find publications that utilize our technology.
3D reconstruction of SARS-CoV-2 infection in ferrets emphasizes focal infection pattern in the upper respiratory tract
Luca M. Zaeck, David Scheibner, Julia Sehl, Martin Müller, Donata Hoffmann, Martin Beer, Elsayed M. Abdelwhab, Thomas C. Mettenleiter, Angele Breithaupt, Stefan Finke
DOI: 10.1101/2020.10.17.339051
Date: 18 October 2020
Methods: Light sheet microscopy, clearing, confocal laser scanning microscopy
Tags: host-pathogen interactions, respiratory tract infection, SARS-CoV-2, COVID-19, 3D immunofluorescence
Product: arivis Vision4D
Effects of cooling rate and oxygen partial pressure on heterogeneous crystal nucleation of supercooled lithium disilicate melt in PtRh20 containers
R. Al-Mukadam, J. Deubener
DOI: 10.1016/j.jnoncrysol.2019.119642
Journal: Journal of Non-Crystalline Solids, Volume 524, 15 November 2019
Product: arivis Vision4D
Translocator protein localises to CD11b+ macrophages in atherosclerosis
Chantal Kopecky Elvis Pandzic, Arvind Parmar, Jeremy Szajer, Victoria Lee, Alexander Dupuy, Andrew Arthur, Sandra Fok, Renee Whan, William J. Ryder, Kerry-Anne Rye, Blake J. Cochran
DOI: 10.1016/j.atherosclerosis.2019.03.011
Journal: Atherosclerosis, Volume 284, May 2019
Methods: Light sheet microscopy, clearing, antibody staining, CT, PET, Mathworks
Tags: stitching, rendering, visualization
Product: arivis Vision4D
Depth-profiling of nickel nanocrystal populations in a borosilicate glass – A combined TEM and XRM study
L.C.Briese, S.Selle, C.Patzig, J.Deubener, T.Höche
DOI: 10.1016/j.ultramic.2019.06.004
Journal: Ultramicroscopy, Volume 205, October 2019
Methods: TEM, STEM-HAADF, XRM, EDXS
Tags: glass, microstructure, materials, distribution, particles, analysis, analysis panel, distances, blob finder
Product: arivis Vision4D
Transgenesis and web resources in quail
Olivier Serralbo, David Salgado, Nadège Véron, Caitlin Cooper, Marie-Julie Dejardin, Timothy Doran, Jérome Gros, Christophe Marcelle
DOI: 10.7554/eLife.56312
Journal: eLife 2020; 9:e56312
Product: arivis Vision4D
High-resolution 3D imaging of fixed and cleared organoids
Johanna F. Dekkers, Maria Alieva, Lianne M. Wellens, Hendrikus C. R. Ariese, Paul R. Jamieson, Annelotte M. Vonk, Gimano D. Amatngalim, Huili Hu, Koen C. Oost, Hugo J. G. Snippert, Jeffrey M. Beekman, Ellen J. Wehrens, Jane E. Visvader, Hans Clevers & Anne C. Rios
DOI: 10.1038/s41596-019-0160-8
Journal: Nature, 03 May 2019
Product: arivis Vision4D
Light sheet fluorescence microscopy guided MALDI-imaging mass spectrometry of cleared tissue samples
Andreas Blutke, Na Sun, Zhihao Xu, Achim Buck, Luke Harrison, Sonja C. Schriever, Paul T. Pfluger, David Wiles, Thomas Kunzke, Katharina Huber, Jürgen Schlegel, Michaela Aichler, Annette Feuchtinger, Kaspar Matiasek, Stefanie M. Hauck & Axel Walch
DOI: 10.1038/s41598-020-71465-1
Journal: Nature, 02 September 2020
Methods: Light sheet microscopy, Visualization: side-by-side view and clipping planes to find landmarks; Volume Fusion to merge the images together
Product: arivis Vision4D
Bioimage Analysis Tools
Kota Miura, Sébastien Tosi, Christoph Möhl, Chong Zhang, Perrine Paul-Gilloteaux, Ulrike Schulze, Simon Norrelykke, Christian Tischer, Thomas Pengo
URL: https://hal.archives-ouvertes.fr/hal-02910986/
Journal: Science, 3 August 2020
Methods: Visualization, segmentation, quantitative 3D and 4D image analysis
Product: arivis Vision4D, arivis WebView
Efficient Skeleton Editing in a VR Environment Facilitates Accurate Modeling of Highly Branched Mitochondria
Ryan Conrad, Thomas Ruth, Falko Löffler, Steffen Hadlak, Sebastian Konrad, Christian Götze, Christopher Zugates, Molly McQuilken, Kedar Narayan
DOI: 10.1017/S1431927620017158
Journal: Cambridge University Press, 30 July 2020
Product: arivis VisionVR
Label‐Free Four‐Dimensional Visualization of Anaerobically Growing Electroactive Biofilms
Christin Koch, Anne Kuchenbuch, Maria Marosvölgyi, Klaus Weisshart, Falk Harnisch
DOI: 10.1002/cyto.a.24169
Journal: Cytometry, 8 June 2020
Methods: Light sheet microscopy
Product: arivis Vision4D
Correlative Nano‐Computed Tomography and Focused Ion‐Beam Sectioning: A Case Study on a Co‐Base Superalloy Oxide Scale
Malte Lenz, Janis Wirth, Silvan Englisch, Jan Rosiwal, Nadine Buchinger, Martin Weiser, Sannakaisa Virtanen, Benjamin, Apeleo Zubiri, Erdmann Spiecker
Journal: Advanced Engineering Materials, Volume 22, Issue 4, April 2020
Methods: Visualization, segmentation, and quantitative 3D analysis, Segmentation of pores in the 3D volume
Product: arivis Vision4D
Maternal high-fat diet during lactation reprograms the dopaminergic circuitry in mice
R.N. Lippert, S. Hess, P. Klemm, L.M. Burgeno, T. Jahans-Price, M.E. Walton, P. Kloppenburg, J.C. Brüning
DOI: 10.1172/JCI134412
Journal: The Journal of Clinical Investigation, 8 June 2020
Product: arivis Vision4D
Red Blood Cells Segmentation: A Fully Convolutional Network Approach
Ario Sadafi, Martin Radolko, Iosif Serafeimidis, Steffen Hadlak
DOI:10.1109/BDCloud.2018.00134
Journal: IEEE, 21 March 2019
Product: arivis Vision4D
Large Area SEM Backscatter Imaging of GABA Post-Embedding Immunogold, Web-Based Crowdsourcing Segmentation and Local Image Processing for Rigorous Quantification
Cheryl Clarkson, Christopher T. Zugates, Christine A. Brantner, Matthias Rust, Anastas Popratiloff
Journal: Cambridge University Press, 05 August 2019
Product: arivis Vision4D, arivis WebView
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Axonal debris accumulates in corneal epithelial cells after intraepithelial corneal nerves are damaged: A focused Ion Beam Scanning Electron Microscopy (FIB-SEM) study
Paola Parlanti, Sonali Pal-Ghosh, Alexa Williams, Gauri Tadvalkar, Anastas Popratiloffa, Mary Ann Stepp
DOI:10.1016/j.exer.2020.107998
Journal: Experimental Eye Research, 21 March 2020
Product: arivis Vision4D
Machine learning analysis of whole mouse brain vasculature
Mihail Ivilinov Todorov, Johannes Christian Paetzold, Oliver Schoppe, Giles Tetteh, Suprosanna Shit, Velizar Efremov, Katalin Todorov-Völgyi, Marco Düring, Martin Dichgans, Marie Piraud, Bjoern Menze & Ali Ertürk
Journal: Nature Methods (2020), 11 March 2020
Methods: Light sheet microscopy; VesSAP-a novel machine learning technology to segment complete mouse brain vasculature
Product: arivis Vision4D, arivis VisionVR
High strength in combination with high toughness in robust and sustainable polymeric materials
Xiaojian Liao, Martin Dulle, Juliana Martins de Souza e Silva, Ralf B. Wehrspohn, Seema Agarwal, Stephan Förster, Haoqing Hou, Paul Smith, Andreas Greiner
Journal: Science 13 Dec 2019: Vol. 366, Issue 6471, pp. 1376-1379
Product: arivis Vision4D, arivis VisionVR
Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells
David P. Hoffman, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen, David J. Solecki, Eric Betzig, Harald F. Hess
Journal: Science 366 published 17 January 2020, eaaz5357 (2020)
Methods: Lattice light sheet microscopy
Product: Channel alignment corrections in arivis Vision4D - Data Transformation Gallery
Peripheral (not central) corneal epithelia contribute to the closure of an annular debridement injury
Mijeong Park, Alexander Richardson, Elvis Pandzic, Erwin P. Lobo, J. Guy Lyons, Nick Di Girolamo
Journal: Proceedings of the National Academy of Sciences Dec 2019, 116 (52) 26633-26643, first published December 16, 2019
Methods: Light-Sheet and Confocal Microscopy; corneas of confetti mice
Product: merged using a maximum intensity projection, and analyzed with arivis Vision4D
Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body
Chenchen Pan, Oliver Schopp, Arnaldo Parra-Damas, Ruiyao Cai, Mihail Ivilinov Todorov, Gabor Gondi, Bettina von Neubeck, Nuray Böğürcü-Seidel, Sascha Seidel, Katia Sleiman, Christian Veltkamp, Benjamin Förstera, Hongcheng Mai, Zhouyi Rong, Omelyan Trompak, Alireza Ghasemigharagoz, Madita Alice Reimer, Angel M. Cuesta, Javier Coronel, Irmela Jeremias, Dieter Saur, Amparo Acker-Palmer, Till Acker, Boyan K. Garvalov, Bjoern Menze, Reinhard Zeidler, Ali Ertürk
DOI: 10.1016/j.cell.2019.11.013
Journal: Cell, Volume 179, ISSUE 7, P1661-1676.e19, December 12, 2019
Methods: vDISCO, Deep learning-based pipeline for comprehensive analysis of metastases - DeepMACT.
Product: Volume Fusion made with arivis Vision4D
Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Korchynska S, Krassnitzer M, Malenczyk K, Prasad RB, Tretiakov EO, Rehman S, Cinquina V, Gernedl V, Farlik M, Petersen J, Hannes S, Schachenhofer J, Reisinger SN, Zambon A, Asplund O, Artner I, Keimpema E, Lubec G, Mulder J, Bock C, Pollak DD, Romanov RA, Pifl C, Groop L, Hökfelt TG, Harkany T.
DOI: 10.15252/embj.2018100882
PMID: 31750562; PMCID: PMC6939201
Journal: EMBO J. 2020 Jan 2;39(1):e100882, Epub Nov 21, 2019
Methods: Optical tissue clearing, pancreas visualization by light‐sheet microscopy
Product: Three‐dimensional‐rendered images were visualized with arivis Vision4D, quantitative analysis
Orthopedic Surgery Triggers Attention Deficits in a Delirium-Like Mouse Model
Velagapudi R, Subramaniyan S, Xiong C, Porkka F, Rodriguiz RM, Wetsel WC, Terrando N.
Orthopedic Surgery Triggers Attention Deficits in a Delirium-Like Mouse Model. Front Immunol. 2019 Nov 19;10:2675.
DOI:10.3389/fimmu.2019.02675
PMID: 31911786; PMCID: PMC6918861
Journal: Frontiers in Immunology Front Immunol. 19 Nov 2019; 10:2675.
Methods: 3D light sheet microscopy, CLARITY, neuroinflammation and blood-brain barrier
Product: high resolution 3D renderings and movies were produced with arivis Vision4D
Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution
Tonmoy Chakraborty, Meghan K. Driscoll, Elise Jeffery, Malea M. Murphy, Philippe Roudot, Bo-Jui Chang, Saumya Vora, Wen Mai Wong, Cara D. Nielson, Hua Zhang, Vladimir Zhemkov, Chitkale Hiremath, Estanislao Daniel De La Cruz, Yating Yi, Ilya Bezprozvanny, Hu Zhao, Raju Tomer, Rainer Heintzmann, Julian P. Meeks, Denise K. Marciano, Sean J. Morrison, Gaudenz Danuser, Kevin M. Dean & Reto Fiolka
Journal: Nature methods
Methods: Animal Specimens, data acquisition ctASLM
Product: 3D renderings were produced with arivis Vision4D
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Scalable Imaging Science Tools to Support Increasingly Efficient Workflows for Research Tasks on Massive Images
Christian Goetze, Christopher T. Zugates, Thomas Ruth, Paul Boenisch, Adam Brady-Myerov
Journal: Cambridge University Press, 05 August 2019
Methods: Extract and share information from high dimensional image data (10 TP per dataset) with ExLLSM
Product: New rendering techniques and creating mask segments in VR solution arivis VisionVR
Tau oligomers mediate aggregation of RNA‐binding proteins Musashi1 and Musashi2 inducing Lamin alteration
Montalbano M, McAllen S, Sengupta U, Puangmalai N, Bhatt N, Ellsworth A, Kayed R.
DOI:10.1111/acel.13035
PMID: 31532069; PMCID: PMC6826126.
Journal: Aging Cell. 2019 Dec;18(6):e13035. Epub 18 September 2019
Methods: Mechanism leading to Neurodegeneration in Alzheimer's disease, immunofluorescence
Product: 3D rendering (volumetric rendering), visualization, and segmentation with arivis Vision4D
Male meiotic spindle features that efficiently segregate paired and lagging chromosomes
Gunar Fabig, Robert Kiewisz, Norbert Lindow, James A. Powers, Vanessa Cota, Leslie Mateo, Jan Brugués, Steffen Prohaska, Diana S. Chu, Thomas Müller-Reichert
DOI:10.1101/737494
Journal: bioRxiv 737494; 19 August 2019
Methods: Analysis of spindle dynamics with confocal light microscopy, Super-resolution fluorescence microscopy, Electron microscopy
Product: arivis Vision4D-Image processing, Cropping, Analysis and segmentation of spindle poles, a custom-made python script
3D-Imaging of Whole Neuronal and Vascular Networks of the Human Dental Pulp via CLARITY and Light Sheet Microscopy
França, C.M., Riggers, R., Muschler, J.L. et al.
Journal: Nature, Sci Rep 9, 10860 (2019)
Methods: 3D light sheet microscopy, CLARITY tissue clearing, human dental pulp
Product: arivis Vision4D, stitching of tiles to create large fields of view, 3D rendering and visualization as 3D volumes and projections
Automated analysis of whole brain vasculature using machine learning
Journal: bioRxiv
Methods: 3D light sheet microscopy, DISCO tissue clearing
Product: arivis Vision4D, arivis VisionVR: renderings of whole mouse brain
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.
DOI: 10.7554/eLife.42434.
PubMed PMID: 30950395; PubMed Central PMCID: PMC6450669.
Journal:Elife. 2019 Apr 5;8:e42434.
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 arivis Vision4D
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.
DOI: 10.1038/s41467-019-09540-z.
PubMed PMID: 30979871; PubMed Central PMCID: PMC6461694.
Journal: Nat Commun. 2019 Apr 12;10(1):1703.
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.
DOI: 10.1038/s42003-019-0337-2.
PubMed PMID: 30854484; PubMed Central PMCID: PMC6405929.
Journal: Commun Biol., 7 Mar 2019; 2:92.
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.
DOI: 10.1038/s41418-018-0150-3.
PubMed PMID: 30006609; PubMed Central PMCID: PMC6370798
Journal: Cell Death Differ. 2019 Mar;26(3):580-596. Epub 13 Jul 2018
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.
DOI:10.1242/jcs.225557.
PubMed PMID: 30709970; PubMed Central PMCID: PMC6382012.
Journal: J Cell Sci. 2019 Feb 1;132(3):jcs225557.
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.
DOI:10.3389/fncel.2019.00023.
PubMed PMID: 30809125; PubMed Central PMCID: PMC6380212.
Journal: Front Cell Neurosci., 11 Feb 2019;13:23.
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
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
Journal: Nature Neuroscience volume 22, pages 317–327 (2019), Published: 31 December 2018
Methods: Fluorescence imaging
Product: arivis Vision4D - 4D Viewer
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution
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
Journal: Science 18 Jan 2019, Vol. 363, Issue 6424, eaau8302
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).
Journal: BMC biology, 17(1), 1. Published online 2019 Jan 7
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
DOI:org/10.1016/j.celrep.2018.11.021
Journal: Cell Reports VOLUME 25, ISSUE 10, P2668-2675.E3, DECEMBER 04, 2018
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
DOI: 10.3324/haematol.2018.199083
Journal: Haematologica Dec 2018, 103 (12) 1997-2007
Methods: Confocal microscopy
Product: arivis Vision4D - 4D Viewer: 3D 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)
DOI:10.1016/j.bonr.2018.11.002
Journal: Bone reports, 9, Dec 2018, 188-198.
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
Journal: J Cell Biol Nov 2018, 217 (11) 3873-3885;
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.
DOI: 10.3390/ijms19113500
Journal: International Journal of Molecular Sciences 19, no. 11: 3500, published: 7 November 2018
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
DOI: 10.1523/JNEUROSCI.0819-18.2018
PubMed 30143572
Journal: The Journal of Neuroscience 10 October 2018, 38 (41) 8723-8736;
Methods: Confocal microscopy, CLARITY
Product: arivis Vision4D - 4D Viewer: 3D 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).
Journal: Molecular Brain 2018, 11:50. Published: 12 September 2018
Methods: Light-sheet fluorescence microscopy, CUBIC
Product: arivis Vision4D - 4D Viewer: 3D 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)
Journal: Molecular biology of the cell, Aug 8; 29(16).29(16), 1963-1974.
Methods: Laser-scanning confocal microscopy
Product: arivis Vision4D - 4D Viewer: 3D 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
DOI: 10.1038/d41586-018-07336-7
Journal: Nature 563, 305-306 (2018) Preprint on BioRxiv, July 23, 2018
Methods: Light-sheet fluorescence microscopy, vDISCO
Product: arivis Vision4D - Tile Sorter: Alignment & Stitching; Scope Fusion, 4D Viewer: 3-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.
DOI: 10.1038/s41598-018-29460-0.
PubMed PMID: 30038304; PubMed Central PMCID: PMC6056470.
Journal: Sci Rep. 2018 Jul 23;8(1):11095.
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
Journal: Science 13 Jul 2018: Vol. 361, Issue 6398, pp. 189-193
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
DOI: 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 Reports, 8, 9545.
DOI: 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 Medicine, 9(374), eaah7029.
DOI: 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.
DOI: 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.
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
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 the detection of feature points in frame images (time series) that greatly reduced the detection of questionable positive signals coming from the 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).
DOI: 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 localization 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
Product: arivis 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
Product: arivis 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 17 Aug 2017
DOI: https://doi.org/10.1371/journal.pone.0183336
Methods: Light-sheet fluorescence microscopy
Product: arivis 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
Product: arivis 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
Product. arivis 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
Product: arivis 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. 2016, 17, 1925.
DOI: https://doi.org/10.3390/ijms17111925
Methods: Light-sheet fluorescence microscopy
Product. arivis 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
Product: arivis 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
Product: arivis 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
Product: arivis 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
Product: arivis 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
Journal: 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
Journal: 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 the 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
Journal: 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
Journal: 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
