PUBLICATIONS

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.

Long-term live imaging of epithelial organoids and corresponding multiscale analysis reveal high heterogeneity and identify core regulatory principles

Lotta Hof, Till Moreth, Michael Koch, Tim Liebisch, Marina Kurtz, Julia Tarnick, Susanna M. Lissek, Monique M.A. Verstegen, Luc J.W. van der Laan, Meritxell Huch, Franziska Matthäus, Ernst H.K. Stelzer, Francesco Pampaloni

DOI: 10.1101/2020.07.12.199463

Journal: bioRxiv

Applications: Light-sheet microscopy

Methods: Visualization, analysis

Products: arivis Vision4d


Investigation of heterocellular features of the mouse retinal neurovascular unit by 3D electron microscopy

Mona J. Albargothy, Nadhira N. Azizah, Sarah L. Stewart, Evan P. Troendle, David H. W. Steel, Tim M. Curtis, Michael J. Taggart

DOI: 10.1111/joa.13721

Journal: Journal of Anatomy

Applications: Volume Electron Microscopy

Methods: Visualization, Analysis

Products: arivis Vision4d


Glioblastoma hijacks neuronal mechanisms for brain invasion

Varun Venkataramani, Yvonne Yang, Marc Cicero Schubert, Wolfgang Wick, Thomas Kuner, Frank Winkler

DOI: 10.1016/j.cell.2022.06.054

Journal: Cell

Methods: Visualization, analysis

Products: arivis Vision4d


Tracking and characterization of partial and full epithelial-mesenchymal transition cells in a mouse model of metastatic breast cancer

Fabiana Lüönd, Natascha Santacroce, Christian Beisel, Laurent Guérard, Thomas R.Bürglin, Gerhard Christofori, Nami Sugiyama

DOI: 10.1016/j.xpro.2022.101438

Journal: STAR Protocols

Methods: Visualization, analysis

Products: arivis Vision4d


EZ Clear for simple, rapid, and robust mouse whole organ clearing

Chih-Wei Hsu, Juan Cerda III, Jason M. Kirk, Williamson D. Turner, Tara L. Rasmussen, Carlos P. Flores Suarez, Mary E. Dickinson, Joshua D. Wythe

DOI: 10.1101/2022.01.12.476113

Journal: bioRxiv

Applications: Light-sheet microscopy

Methods: Visualization, analysis

Products: arivis Vision4d


Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization

Daria Amiad-Pavlov, Dana Lorber, Gaurav Bajpai, Adriana Reuveny1, Francesco Roncato, Ronen Alon, Samuel Safran, Talila Volk

DOI: 10.1126/sciadv.abf6251

Journal: Science Advances

Methods: Visualization, 3D image analysis, filtering, segmentation, scripting

Products: arivis Vision4d


Keratin dynamics govern the establishment of the maternal-fetal interface

Wallis Nahaboo, Sema Elif Eski, Marjorie Vermeersch, Bechara Saykali, Daniel Monteyne, Thomas M. Magin, Nicole Schwarz, An Zwijsen, David Perez-Morga, Sumeet Pal Singh, Isabelle Migeotte

DOI: 10.1101/2021.04.07.438772

Journal: bioRxiv

Products: arivis Vision4d


Neuroglia infection by rabies virus after anterograde virus spread in peripheral neurons

Madlin Potratz, Luca M. Zaeck, Carlotta Weigel, Antonia Klein, Conrad M. Freuling, Thomas Müller & Stefan Finke

DOI: 10.1186/s40478-020-01074-6

Journal: Acta Neuropathologica Communications

Products: arivis Vision4d


Chronic sleep loss disrupts blood–testis and blood–epididymis barriers, and reduces male fertility

Emilio Domínguez‐Salazar, Gabriela Hurtado‐Alvarado, Fernanda Medina‐Flores, Javik Dorantes, Oscar González‐Flores, Arturo Contis‐Montes de Oca, Javier Velázquez‐Moctezuma, Beatriz Gómez‐González

DOI: 10.1111/jsr.12907

Journal: Journal of Sleep Research

Products: arivis Vision4d


Visualizing Periocular Mesenchyme Subpopulation Migratory Behaviors During Zebrafish Ocular Anterior Segment Development

Kristyn VanDerMeulen, Jakub Famulski

DOI: https://iovs.arvojournals.org/article.aspx?articleid=2691365

Journal: iovs

Methods: 3D confocal and Light sheet microscopy

Products: arivis Vision4d


B cell dissemination patterns during the germinal center reaction revealed by whole-organ imaging

Liat Stoler-Barak, Adi Biram, Natalia Davidzohn, Yoseph Addadi, Ofra Golani, Ziv Shulman

DOI: 10.1084/jem.20190789

Journal: Journal of Experimental Medicine

Methods: Light sheet microscopy, intravital

Products: arivis Vision4d


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​

Journal: bioRxiv

Methods: Light sheet microscopy, clearing, confocal laser scanning microscopy

Products: 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

Products: 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

Methods: TEM, STEM-HAADF, XRM, EDXS

Products: 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 Protocols

Products: 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: Scientific Reports

Methods: Light sheet microscopy, Visualization: side-by-side view and clipping planes to find landmarks; Volume Fusion to merge the images together

Products: arivis Vision4d


Bioimage Analysis Tools

Kota Miura, Sébastien Tosi, Christoph Möhl, Chong Zhang, Perrine Paul-Gilloteaux, Ulrike Schulze, Simon Norrelykke, Christian Tischer, Thomas Pengo

DOI: https://hal.archives-ouvertes.fr/hal-02910986/

Journal: Science

Methods: Visualization, segmentation, quantitative 3D and 4D image analysis

Products: arivis Vision4d, arivis VisionHub


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

Products: 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

Methods: Light sheet microscopy

Products: 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

DOI: 10.1002/adem.201900823

Journal: Advanced Engineering Materials

Methods: Visualization, segmentation, and quantitative 3D analysis, Segmentation of pores in the 3D volume

Products: 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

Products: 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

Products: 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

DOI: 10.1017/S1431927619007694

Journal: Cambridge University Press

Products: arivis Vision4d, arivis VisionHub


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

Products: 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

DOI: 10.1038/s41592-020-0792-1

Journal: Nature Methods

Methods: Light sheet microscopy; VesSAP-a novel machine learning technology to segment complete mouse brain vasculature

Products: 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

DOI: 10.1126/science.aaz5357​

Journal: Science

Methods: Lattice light sheet microscopy

Products: arivis Vision4d


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

DOI: 10.1073/pnas.1912260116

Journal: Proceedings of the National Academy of Sciences

Methods: Light-Sheet and Confocal Microscopy; corneas of confetti mice

Products: 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

Journal: EMBO J

Methods: Optical tissue clearing, pancreas visualization by light‐sheet microscopy

Products: 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

DOI: 10.1038/s41592-019-0615-4

Journal: Nature Methods

Methods: Animal Specimens, data acquisition ctASLM

Products: arivis Vision4d


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

DOI: 10.1017/S143192761900758X

Journal: Cambridge University Press

Methods: Extract and share information from high dimensional image data (10 TP per dataset) with ExLLSM

Products: 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

Journal: Aging Cell

Methods: Mechanism leading to Neurodegeneration in Alzheimer's disease, immunofluorescence

Products: 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

Methods: Analysis of spindle dynamics with confocal light microscopy, Super-resolution fluorescence microscopy, Electron microscopy

Products: arivis Vision4d


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

Journal: eLife

Methods: Time-lapse confocal microscopy

Products: arivis Vision4d


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

Journal: Communications Biology

Methods: Live time-lapse light sheet microscopy

Products: arivis Vision4d


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

Journal: Journal of Cell Science

Methods: Structured-illumination microscopy

Products: arivis Vision4d


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

DOI: 10.1038/s41593-018-0301-3

Journal: Nature Neuroscience

Methods: Fluorescence imaging

Products: arivis Vision4d


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

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

DOI: 10.1126/science.aau8302

Journal: Science

Methods: Combined expansion and lattice light-sheet microscopy

Products: arivis Vision4d


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.

DOI: 10.1186/s12915-018-0614-4

Journal: BMC biology

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

Products: arivis Vision4d


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.

DOI: 10.1038/s41598-018-27830-2

Journal: Scientific Reports

Methods: spinning disk confocal microscope, multiphoton microscopy

Products: arivis Vision4d


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.

DOI: 10.1126/scitranslmed.aah7029

Journal: Science Translational Medicine

Methods: three-dimensional imaging of solvent-cleared organs (iDISCO) data

Products: arivis Vision4d


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.

DOI: 10.1038/s41598-018-26673-1

Journal: Scientific Reports

Methods: Confocal microscopy

Products: arivis Vision4d


Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions

Janes G, von Wangenheim D, Cowling S, et al.

DOI: 10.3389/fpls.2018.00735

Journal: Frontiers in Plant Science

Methods: Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1126/science.aaq1392​

Journal: Science

Methods: noninvasive lattice light-sheet microscopy combined with aberration-correcting adaptive optics

Products: arivis Vision4d


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

DOI: 10.1038/s41467-018-04419-x

Journal: Nature Communications

Methods: Light-sheet fluorescence microscopy

Products: arivis Vision4d


Expression of HIV-1 pathogenesis factor NEF in CD4 T cells impairs antigen-specific B-cell function

Sheetal Kaw, Swetha Ananth, Nikolaos Tsopoulidis, Katharina Morath, Bahar M Coban, Ralph Hohenberger, Olcay C Bulut, Florian Klein, Bettina Stolp & Oliver T Fackler

DOI: 10.15252/embj.2020105594

Journal: The EMBO Journal

Methods: Visualization, segmentation, Cell Interaction Tracking, quantitative 3D and 4D image analysis

Products: arivis Vision4d, arivis VisionVR


Intravital Assessment of Cells Responses to Conducting Polymer-Coated Carbon Microfibres for Bridging Spinal Cord Injury

Bilal El Waly, Vincent Escarrat, Jimena Perez-Sanchez, Jaspreet Kaur, Florence Pelletier, Jorge Eduardo Collazos-Castro, Franck Debarbieux

DOI: 10.3390/cells10010073

Journal: Cells

Methods: Visualization, segmentation, quantitative 3D and 4D image analysis

Products: arivis Vision4d


Neuronal and vascular deficits following chronic adaptation to high altitude

Nathan P. Cramer, Alexandru Korotcov, Asamoah Bosomtwi, Xiufen Xu, Derek R. Holman, Kathleen Whiting, Scott Jones, Andrew Hoy, Bernard J. Dardzinski, Zygmunt Galdzicki

DOI: 10.1016/j.expneurol.2018.10.007

Journal: Experimental Neurology

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Big Data Approach to Electron Microscopy Acquisition and Analysis of Neuronal Tissue: Utility in Analysis of Neuronal and Synaptic Alterations in a Mouse Model of 22q11 deletion Syndrome

Liz Matsiyevskiy, Anastas Popratiloff, Christine Brantner

DOI: https://hsrc.himmelfarb.gwu.edu/gw_research_days/2017/BME/9/

Journal: DEPARTMENT OF BIOMEDICAL ENGINEERING POSTERS AND PRESENTATIONS

Methods: Electron microscopy

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Post-Embedding Immunogold Detection of GABA-Labeling Using Large Area, High Resolution SEM Backscatter Imaging

Cheryl Clarkson1, Christine A. Brantner, Nancy W. Rizzo, Christopher T. Zugates, Anastas Popratiloff

DOI: 10.1017/S1431927618007419

Journal: Cambridge University Press

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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

Methods: Light sheet microscopy, clearing, antibody staining, CT, PET, Mathworks

Products: 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

Products: arivis Vision4d


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

DOI: 10.1126/science.aay9033

Journal: Science

Products: arivis Vision4d, arivis VisionVR


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

Methods: vDISCO, Deep learning-based pipeline for comprehensive analysis of metastases - DeepMACT.

Products: arivis Vision4d


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.

DOI: 10.3389/fimmu.2019.02675

Journal: Frontiers in Immunology

Methods: 3D light sheet microscopy, CLARITY, neuroinflammation and blood-brain barrier

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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.

DOI: 10.1038/s41598-019-47221-5

Journal: Scientific Reports

Methods: 3D light sheet microscopy, CLARITY tissue clearing, human dental pulp

Products: arivis Vision4d


Automated analysis of whole brain vasculature using machine learning

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

DOI: 10.1101/613257

Journal: bioRxiv

Methods: 3D light sheet microscopy, DISCO tissue clearing

Products: arivis Vision4d, arivis VisionVR


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

Journal: Nature Communications

Methods: Multi-Photon confocal microscopy

Products: arivis Vision4d


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

Journal: Cell Death & Differentiation

Methods: Confocal laser-scanning microscopy

Products: arivis Vision4d


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

Journal: Front Cell Neurosci

Methods: Cellular neuroscience, Fluorescence imaging

Products: arivis Vision4d


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

DOI: 10.1083/jcb.201804137

Journal: Journal of Cell Biology

Methods: Lattice light sheet microscopy

Products: arivis Vision4d


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

Methods: Light-sheet fluorescence microscopy, vDISCO

Products: arivis Vision4d


Whole Organ Blood and Lymphatic Vessels Imaging (WOBLI)

Oren, R., Fellus-Alyagor, L., Addadi, Y., Bochner, F., Gutman, H., Blumenreich, S., … Lazar, S.

DOI: 10.1038/s41598-018-19663-w

Journal: Scientific Reports

Methods: Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1101/198275

Journal: bioRxiv

Methods: Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

Brobeil A, Chehab R, Dietel E, Gattenlöhner S, Wimmer M.

DOI: 10.3390/biom7030055

Journal: biomolecules

Methods: Confocal Laser Scanning Microscopy

Products: arivis Vision4d


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: 10.1016/j.celrep.2018.11.021

Journal: Cell Reports

Methods: Optical kidney clearing, Clarity, confocal microscopy, light-sheet microscopy

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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

Methods: Confocal microscopy

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

Zhu, Y., Ma, Y., & Elefteriou, F.

DOI: 10.1016/j.bonr.2018.11.002

Journal: Bone reports

Methods: Whole mount light sheet microscopy, CLARITY

Products: arivis Vision4d


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.

DOI: 10.3390/ijms19113500

Journal: International Journal of Molecular Sciences

Methods: Light-sheet fluorescence microscopy, CLARITY

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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

Journal: The Journal of Neuroscience

Methods: Confocal microscopy, CLARITY

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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.

DOI: 10.1186/s13041-018-0393-4

Journal: Molecular Biology of the Cell

Methods: Light-sheet fluorescence microscopy, CUBIC

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

Parreno, J., Cheng, C., Nowak, R. B., & Fowler, V. M

DOI: 10.1091/mbc.E18-01-0035

Journal: Molecular biology of the cell

Methods: Laser-scanning confocal microscopy

Products: arivis Vision4d


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.

DOI: 10.1038/s41598-018-29460-0.

Journal: Scientific Reports

Methods: Light-sheet fluorescence microscopy

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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

DOI: 10.1126/science.aar7462

Journal: Science

Methods: Light-sheet fluorescence microscopy

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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

DOI: 10.7554/eLife.33910

Journal: eLife

Methods: volumetric imaging of immunostained whole organs (iDISCO), Lightsheet Microscopy, 2-Photon Microscopy, Confocal Microscopy

Products: arivis Vision4d


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

Hilscher MM, Leão RN, Edwards SJ, Leão KE, Kullander K (2017)

DOI: 10.1371/journal.pbio.2001392

Journal: PLoS Biol

Applications: Neuroscience, Optogenetics

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

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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.

DOI: 10.3390/ijms17111925

Journal: International Journal of Molecular Sciences

Methods: Light-sheet fluorescence microscopy

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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

DOI: 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

Products: arivis Vision4d


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

C.Schmidt, M.Reinehr, O.Leucht, N.Behrendt, S.Geiler, S.Britsch

DOI: 10.1016/j.aanat.2011.04.009

Journal: Annals of Anatomy - Anatomischer Anzeiger

Applications: E-Learning; Microscopic anatomy

Products: arivis VisionHub


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.

DOI: 10.1038/s41589-018-0004-9

Journal: Nature Chemical Biology

Methods: Light-sheet microscopy

Products: arivis Vision4d


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.

DOI: 10.1016/j.molcel.2018.02.007

Journal: Mol Cell

Methods: Confocal super-resolution microscopy

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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.

DOI: 10.1038/s41594-017-0015-3

Journal: Nature Structural & Molecular Biology

Methods: confocal super- resolution microscopy; CRISPR live-cell imaging

Products: arivis Vision4d


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

DOI: 10.1038/s41467-017-00774-3

Journal: Nature Communications

Applications: Confocal Microscopy

Methods: Confocal Microscopy

Products: arivis Vision4d


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

DOI: 10.1016/j.devcel.2017.07.021

Journal: Developmental Cell

Applications: Neurobiology, Developmental Biology

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1242/dev.148684

Journal: Development

Methods: Clarity, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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.

DOI: 10.1371/journal.pone.0183336

Journal: PLoS ONE

Methods: Light-sheet fluorescence microscopy

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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;

DOI: 10.1093/cercor/bhw094

Journal: Cerebral Cortex Oxford Journal

Applications: Neuroscience, cell migration

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1016/j.cell.2016.05.007

Journal: Cell

Applications: Neuroscience: Whole Brain Imaging

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1016/j.cell.2017.07.013

Journal: Cell

Applications: Neuroscience: Whole Brain Imaging, fluorescence

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1016/j.stemcr.2017.07.017

Journal: Stem Cell Reports

Applications: Neuroscience: 3D spheroids

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1038/srep43693

Journal: Scientific Reports

Applications: Cell biology: 3D cell culture, image processing

Methods: Optical clearing techniques, Light-sheet fluorescence microscopy

Products: arivis Vision4d


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

Walker, F. et al.

DOI: 10.1038/ncomms13664

Journal: Nature Communications

Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex

Methods: Confocal microscopy

Products: arivis Vision4d


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

DOI: 10.1038/srep18631

Journal: Scientific Reports

Applications: Neuroscience: Whole BraIn Imaging

Methods: Optical imaging, fluorescence imaging, optical clearing techniques, light-sheet fluorescence microscopy

Products: arivis Vision4d


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

DOI: 10.1093/cercor/bhv257

Journal: Cerebral Cortex Oxford Journal

Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex

Methods: Confocal microscopy

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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

DOI: 10.1007/s00429-014-0866-x

Journal: Springer: Brain Structure and Function

Applications: Neuroscience: Neuroanatomy, neuronal activation, Barrel cortex

Methods: Confocal microscopy

Products: arivis Vision4d


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

Enrico Gutzeit , Christian Scheel , Tim Dolereit and Matthias Rust

DOI: 10.5220/0004648604170424

Journal: Computer Vision Theory and Applications (VISAPP), 2014 International Conference on (Volume:1 )

Applications: Zooplankton

Methods: Inverted light microscopy

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