Installation and citation
System requirements
Microsoft Windows: 64-bit operating system, Windows 7 or later
Apple macOS: OS X 10.9 (Mavericks) or later
3 gigabytes RAM
Display resolution minimum 1440 pixels wide and minimum 650 pixels high.
Technical information
QuickNII consists of two co-located executable components implemented in two programming languages for historical reasons. The GUI component is implemented in MXML+ActionScript (runs on Adobe Integrated Runtime, which is bundled as “captive runtime”, requiring no installation). A slicer service running in the background is implemented in Java (and has a bundled JRE requiring no installation). The two components communicate via standard output and local TCP connections (using the loopback interface).
Download:
Link: https://www.nitrc.org/projects/quicknii/
Unzipp the QuickNII 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: (QuickNII, RRID:SCR_016854)
- -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
QuickNII 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:
QuickNII 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 Common Coordinate Framework version 3 (RRID:JCR_020999 and RRID:JRC_021000)
Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell. 2020 May 14;181(4):936-953.e20. doi: 10.1016/j.cell.2020.04.007. Epub 2020 May 7.
See the citation policy from the Allen Intitute for more information.
Waxholm Atlas of the Sprague Dawley Rat (RRID:SCR_017124)
Please refer to the atlas using RRID:SCR_017124, specify the atlas version(s) used, and cite the most recent publication:
Kleven, H., Bjerke, I.E., Clascá, F. et al. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods 20, 1822–1829 (2023). DOI: 10.1038/s41592-023-02034-3
If your work makes use of previous atlas versions, or brain region descriptions detailed in earlier publications, please also cite the corresponding publication:
Version 1: Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386. DOI: 10.1016/j.neuroimage.2014.04.001
Version 2: Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108, 441-449. DOI: 10.1016/j.neuroimage.2014.12.080
Version 3: Osen KK, Imad J, Wennberg AE, Papp EA, Leergaard TB (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. DOI: 10.1016/j.neuroimage.2019.05.016
Release notes
Version 2.2 (2019-05-28) This release includes several new reference atlases: ABAMouse-v3-2017 and WHSRat-v3 both with Mac and Windows.
Linux support was added in July 2020.
Version 2.2preview (2019-04-02) Series descriptor builder recognizes multiple numbering variants in filenames (numbers at fixed character position from either end of names, and sequence indicator _s prefixanywhere)
Coordinate transformation to/from Allen CCFv3 added to Mouse package.
Version 2.1 (2018-12-05) First stable version