**What is MeshView?**
===================== 
MeshView is one of several tools developed by by the NeSys laboratory at University of Oslo with the aim of facilitating brain atlas-based analysis and integration of experimental data and knowledge about the human and rodent brain.
MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain.


.. image:: 483026fbdc47496f8b140360f8bcbb0c/media/image16.png
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*Key features*:
  - orbiting view with toggleable opaque/transparent/hidden parcellation meshes
  - rendering user defined cut surface as if meshes were solid objects
  - rendering point-clouds (simple type-in, or loaded from a JSON format which is typically obtained from the Nutil tool in the QUINT workflow)
  - coordinate system is compatible with QuickNII (https://quicknii.readthedocs.io)

.. tip:: 
   **MeshView can be used to visualize output from the QUINT workflow**
   
   Visit `EBRAINS <https://ebrains.eu/service/quint/>`_ for more information about QUINT. Find full user documentation `here <https://quint-workflow.readthedocs.io>`_. 

**Which atlases are supported?**
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. Allen Mouse Brain Atlas Common Coordinate Framework version 3 (2015 and 2017) (CCFv3) (Wang et al. 2020. Cell, https://doi.org/10.1016/j.cell.2020.04.007. Epub 2020 May 7; RRID:JCR_020999 and RRID:JRC_021000) 
2. Waxholm Atlas of the Sprague Dawley rat, version 2, 3 and 4 (WHS rat brain atlas) (Kjonigsen LJ, et al. (2015) NeuroImage 108, 441-449. DOI: 10.1016/j.neuroimage.2014.12.080j; Osen et al. 2019. NeuroImage, https:doi.org/10.1016/j.neuroimage.2019.05.016; Kleven et al. Nat Methods, 2020. https://doi.org/10.1038/s41592-023-02034-3; RRID:SCR_017124)


**What is the output of MeshView?**
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- Visualisation of a point cloud file file (JSON format) containing the coordinates of objects segmented out from section images in atlas space and atlas meshes. By using the "screenshot" button, users can obtain a png image file of the main window field of view.

- The configuration of the current view using the "configuration" button can be exported and reused