Cite us

QUINT workflow

  • Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU,Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG. QUINT: Workflow for quantification and spatial analysis of features in histological images from rodent brain. Front Neuroinform. 2019 Dec 3;13:75. https://doi.org/10.3389/fninf.2019.00075.

QuickNII (RRID:SCR_016854)

  • Puchades MA, Csucs G, Lederberger D, Leergaard TB and Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796

DeepSlice

  • Carey H., Pegios M., Martin L., Saleeba C., Turner A.J., Everett N.A., Bjerke I.E., Puchades M.A., Bjaalie J.G., McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. Nat Commun 14, 5884 (2023). https://doi.org/10.1038/s41467-023-41645-4

Ilastik (RRID:SCR_015246)

  • Berg S., Kutra D., Kroeger T., Straehle C.N., Kausler B.X., Haubold C., et al. (2019) ilastik:interactive machine learning for (bio) image analysis. Nat Methods. 16, 1226–1232. https://doi.org/10.1038/s41592-019-0582-9

Nutil (RRID: SCR_017183)

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

VisuAlign (RRID:SCR_017978)

  • Puchades MA, Csucs G, Lederberger D, Leergaard TB and Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796

  • 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. Commun Biol. 2024 May 20;7(1):605. https://doi.org/10.1038/s42003-024-06242-1.

MeshView (RRID:SCR_017222)

  • 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

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. Commun Biol. 2024 May 20;7(1):605. https://doi.org/10.1038/s42003-024-06242-1.

Cite the atlases

Allen Mouse Brain Atlas Common Coordinate Framework version 3

Check the Allen Institute citation policy.

Waxholm Space 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 et al (2023). Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods. 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

Kim Unified Adult Mouse Brain Atlas

  • Chon, U., Vanselow, D.J., Cheng, K.C. et al. Enhanced and unified anatomical labeling for a common mouse brain atlas.

Nat Commun 10, 5067 (2019). https://doi.org/10.1038/s41467-019-13057-w

Developmental Mouse Brain Atlas

We encourage researchers who use DeMBA to cite both the dataset and publication presenting DeMBA, and to specify the age of any template(s) used and the version of any segmentation(s) used.