Conditions of use

Nutil is an integral part of the QUINT workflow, and is developed by the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway.

Authors: Nicolaas E Groeneboom, Sharon C. Yates, Maja A. Puchades, Jan G. Bjaalie.

Licence: GNU General Public License version 3.

Acknowledgements: Nutil was developed with support from the EBRAINS infrastructure, and 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

  • Nutil: Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Postprocessing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 14:37. doi: 10.3389/fninf.2020.00037

  • QUINT workflow: Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn P-H, Demuth H-U, HartlageRübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA and Bjaalie JG (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: 10.3389/fninf.2019.00075.

How to cite the reference atlases

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.

See the citation policy from the Allen Intitute for more information.

Waxholm Space atlas of the Sprague Dawley rat brain version 2 , 3 and 4 (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

For reuse of the Waxholm Space atlas of the Sprague Dawley rat brain, see the citation policy.