Version 55.1 by puchades on 2020/09/24 11:43
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1 [[image:QUINT_workflow_Plaques.png||style="float:left"]]
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3 == (% style="color:#c0392b" %)**Description**(%%) ==
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5 **The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
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7 **Examples of use are: cell counting and spatial distributions; determination of projection areas in connectivity experiments; exploration of pathological hallmarks in brain disease models. Integration of various data to the same reference space enables new exploration strategies and re-use of experimental data.**
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9 The workflow is built on the following open access software:
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11 * [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells, using machine learning image segmentation.
12 * [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates custom-angle slices from volumetric brain atlases to match the proportions and cutting plane of histological sections.
13 * //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) is then used for nonlinear alignment of the reference atlas slice to the section image..
14 * (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of //ilastik// and //QuickNII//.
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16 In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
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18 [[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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34 QUINT workflow video
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36 == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
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40 The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
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46 As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
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49 ==== (% style="color:#c0392b" %)**References**(%%) ====
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51 * Yates SC et al. 2019. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
52 * Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
53 * Berg S, Kutra D, Kroeger T, et al. & Kreshuk A (2019) ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 16:1226-1232. doi: [[10.1038/s41592-019-0582-9>>attach:https://www.nature.com/articles/s41592-019-0582-9]]
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55 Puchades MA et al. (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>>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216796]]
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58 ==== (% style="color:#c0392b" %)**User support**(%%) ====
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60 * [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
61 * [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
62 * [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
63 * [[ilastik>>https://www.ilastik.org/]]
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