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Quality control of histological images and their atlas registration

  • Interactive tool tailored for data quality control in the QUINT workflow
  • Verification of atlas registration accuracy
  • Exploration of atlas hierarchies and creation of customized atlas levels

QCAlign was developed to support the use of the QUINT workflow for high-throughput studies. The QUINT workflow supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to a reference atlas.

Related publications

  • Puchades M.A., Csucs G., Ledergerber D., Leergaard T.B., Bjaalie J.G. (2019) Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PlosOne. 14(5) : e0216796. doi: 10.1371/journal.pone.0216796
  • 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. doi: 10.3389/fninf.2019.00075
  • 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. doi: 10.3389/fninf.2020.00037
  • 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.
  • Leergaard, Trygve B. & Bjaalie, Jan G. (2022). Atlas-based data integration for mapping the connections and architecture of the brain. Science. ISSN 0036-8075. 378(6619), s. 488–492. doi: 10.1126/science.abq2594

Other software

All software

Extract, quantify and analyse features from rodent histological images

The QUINT workflow comprises a suite of software designed to support atlas-based quantification. All the software have user interfaces, with no coding ability required. It generates object counts and percentage coverage per atlas-region, in addition to point clouds for visualising the features in 3D.

Brain atlases

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