How to access

The QUINT-online workflow is under development. To access a beta version, go to the QUINT-online workflow, register for an EBRAINS account, and login. As it is currently under development, use for testing purposes only. Feedback is appreciated and will help improve the user experience.

Tip

A mature version of the QUINT workflow is available through the use of a series of standalone desktop applications, learn more here (QuickNII, VisuAlign, ilastik and Nutil). QUINT online is being developed to provide tighter integration of the tools and benefits such as microscopy viewer links and automated plotting.

System requirements

The QUINT-online workflow is accessible with an EBRAINS account using the web browsers: Firefox, Edge and Chrome.

Conditions of use

Licence: Source code: MIT License.

Citation: An article about the QUINT-online workflow is in preparation. Until this is published, please cite our latest article about our software and pipelines (Puchades et al, 2025) for use of our online tools. For use of our standalone software, please cite the relevant articles listed below.

All reference atlases used should also be cited.

Latest article about our software and pipelines

  • Puchades M, Yates SC, Csucs G, Carey H, Balkir A, Leergaard T, Bjaalie J. Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. Frontiers of Neuroinformations. 2025. https://doi.org/10.3389/fninf.2025.1629388

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, 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 (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

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