Installation and citation

Availabe for download here: https://www.nitrc.org/projects/qcalign

QCAlign is downloaded as a zip archive file and can be extracted and run anywhere on the computer by double click on “QCAlign.bat”.

Basic information

QCAlign supports systematic post-processing of the QUINT results. It was developed by the Neural Systems Laboratory at the Institute of Basic Medical Sciences at the University of Oslo in Norway, in collaboration with the Kaczorowski Lab at the Jackson Laboratory in Bar Harbor, Maine, in the USA.

Conditions of use

GNU General Public License version 3.

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

Acknowledgements

QCAlign was developed with support from the EBRAINS infrastructure, with funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).

How to cite QCAlign

RRID:SCR_023088

Gurdon B, Yates SC, Csusc G, Groeneboom N, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O’Connell K, Singh S, Murdy T, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard T, Puchades M, Bjaalie J, Kaczorowski C (2023). Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model. BioRxiv. DOI: 10.1101/2023.02.27.530226

How to cite the reference atlases

Allen Mouse Brain Atlas Common Coordinate Framework version 3

  • 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.

Check the Allen insitute citation policy.

Waxholm Atlas of the Sprague Dawley Rat

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

Contact us

email: support@ebrains.eu