Cite us

QUINT

  • 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, Everett N, Puchades M, Bjaalie J, McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. BioRxiv. https://doi.org/10.1101/2022.04.28.489953

ilastik

  • 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

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. BioRxiv. DOI: 10.1101/2023.02.27.530226.

Cite the 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. PMID: 32386544; PMCID: PMC8152789.

Waxholm Atlas of the Sprague Dawley Rat version 2, version 3 and version 4 (RRID: SCR_017124)

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