Installation requirements

System requirements

VisuAlign uses files generated for and by QuickNII. VisuAlign therefore has the same image requirements as QuickNII:

Standard web-compatible image formats are supported, 24-bit PNG and JPEG.

Images can be loaded up to the resolution of 16 megapixels (e.g. 4000x4000 or 5000x3000 pixels). However, just like QuickNII, VisuAlign does not benefit from image resolutions exceeding the resolution of the monitor in use. For a standard FullHD or WUXGA display (1920x1080 or 1920x1200 pixels) the useful image area is approximately 1500x1000 pixels, using a similar resolution ensures optimal image-loading performance and also eliminates excess storage size. As fulfilling these requirements usually requires preprocessing of the images (converting to PNG or JPEG and downscaling to screen-like size),

VisuAlign keeps track of original image dimensions as part of its series descriptor.

Technical information

comming soon..

Download:

Link: https://www.nitrc.org/projects/visualign

Unzipp the VisuAlign folder at your desired location.

Conditions of use

Licence:

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International for the main component. Source code: MIT License.

Citation of the tool:

-RRID on SciCrunch: (VisuAlign, RRID:SCR_017978)

-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

VisuAlign 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:

VisuAlign 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

Release notes

*Version 0.9 (2021-10-11)

*Version 0.8 (2020-01-23) First stable version