Installation requirements
System requirements
Web application for realtime 3D display of mesh-data representing structural parcellations, and generation of user defined cut planes. Any web browser can be used.
Technical information
WebAlign can be used directly (see links further down) but is also available as a webservice on EBRAINS. Please consult these page if you want to analyse your our data and generate point clouds representing your data: https://www.ebrains.eu/brain-atlases/analysis/image-annotation-and-export-of-coordinate-points; https://www.ebrains.eu/brain-atlases/analysis/labelled-features-analysis.
Conditions of use
Licence:
Source code: MIT License.
Citation of the tool:
-RRID on SciCrunch: (MeshView, RRID:SCR_017222)
- -Puchades MA, Csucs G, Ledergerber D, Leergaard TB, Bjaalie JG (2019)
Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLOS ONE 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796
Cite funding
MeshView is developed at the Neural Systems Laboratory, Institute of Basic Medical Sciences,University of Oslo (Norway), with funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
Citation of the atlases embedded in the tool:
MeshView can be used with the following reference atlases:
Allen Mouse Brain Atlas version 3 2015 Allen Mouse Brain Atlas version 3 2017 Waxholm Space Atlas of the Sprague Dawley rat v2 Waxholm Space Atlas of the Sprague Dawley rat v3 Waxholm Space Atlas of the Sprague Dawley rat v4 |
How to cite:
Allen Mouse Brain Atlas (@ 2004 Allen Institute for Brain Science. Allen Mouse Brain Atlas. Available from:
http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/).
Waxholm Space atlas of the Sprague Dawley rat brain
version 1.01,2,3 and 4 (RRID: SCR_017124; Papp et al.,NeuroImage 97, 374-386, 2014; Papp et al., NeuroImage 105, 561–562, 2015; Kjonigsen et al., NeuroImage 108, 441-449, 2015; Osen et al., NeuroImage 199, 38-56, 2019; Kleven et al., in preparation)
For reuse of the Waxholm Space atlas of the Sprague Dawley rat brain,see citation policy at https://www.nitrc.org/citation/?group_id=1081
Links
[Waxholm Space Atlas of the Sprague Dawley Rat Brain v2](https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v2_39um) - hierarchical, 80 visible structures, with “inner ear”
[Waxholm Space Atlas of the Sprague Dawley Rat Brain v3](https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v3_39um) - hierarchical, 118 visible structures
[Waxholm Space Atlas of the Sprague Dawley Rat Brain v4](https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v4_39um) - hierarchical, 222 visible structures
[Allen Mouse Brain Atlas CCFv3 2015](https://meshview.apps.hbp.eu/?atlas=ABA_Mouse_CCFv3_2015_25um) - hierarchical, color-reduced version, 211 visible structures, with “root” (transparent at start)
[Allen Mouse Brain Atlas CCFv3 2017](https://meshview.apps.hbp.eu/?atlas=ABA_Mouse_CCFv3_2017_25um) - hierarchical, 670 visible structures, with “root” (transparent at start)
[Allen Mouse Brain Atlas CCFv3 root](https://meshview.apps.hbp.eu/?atlas=AMBA_CCFv3_root) - root structure only (brain outline)
Release notes
Current version: MeshView 0.8h