The QUINT workflow comprises a flexible suite of software designed to support atlas-based quantification of labelled features in series of histological images from mouse or rat brain.
- QuickNII (Semi-automated Linear Atlas-Registration)
- VisuAlign (Nonlinear Refinement of Atlas-Registration)
- DeepSlice (Automated Atlas-Registration)
- QCAlign (Quality Control)
- ilastik software (Image Segmentation)
- Nutil software (Quantification)
- Meshview (3D Viewer)
https://quint-workflow.readthedocs.io/
The tools in the QUINT workflow were developed with support from the EBRAINS infrastructure, and funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
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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.
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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
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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
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QCAlign (RRID:SCR_023088). Gurdon B, Yates SC, et al. Investigating cellular diversity in a novel mouse model of Alzheimer’s disease. Manuscript in preparation.
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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
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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
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VisuAlign (RRID:SCR_017978). Gurdon B, Yates SC, et al. Investigating cellular diversity in a novel mouse model of Alzheimer’s disease. Manuscript in preparation.
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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