QCAlign

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

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Publication

Atlas-based data integration for mapping the connections and architecture of the brain

Leergaard, Trygve B. & Bjaalie, Jan G. (2022) Science. ISSN 0036-8075. 378(6619), s. 488–492.
Publication

Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

Groeneboom N.E., Yates S.C., Puchades M.A. and Bjaalie J.G. (2020) Front. Neuroinform. 14:37
Publication

QUINT: Workflow for quantification and spatial analysis of features in histological images from rodent brain

Yates S.C., Groeneboom N.E., Coello C., Lichtenthaler S.F., Kuhn P.H., Demuth H.U., Hartlage-Rübsamen M., Roßner S., Leergaard T., Kreshuk A., Puchades M.A., Bjaalie JG. (2019) Front. Neuroinform. 13, 75
Publication

Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool

Puchades M.A., Csucs G., Lederberger D., Leergaard T.B., and Bjaalie J.G. (2019) PLosONE. 14 (5): e0216796
Publication

ilastik: interactive machine learning for (bio) image analysis

Berg S., Kutra D., Kroeger T., Straehle C.N., Kausler B.X., Haubold C., et al. (2019). Nat Methods. 16, 1226–1232
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Source Code
Contributors
JGB SCY CK BG MAP GC

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