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| 1 | (% style="text-align:center" %) | ||
| 2 | [[image:QUINT_workflow_pic.png||height="394" width="1011"]] | ||
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| 4 | == (% style="color:#c0392b" %)**Workflow Description**(%%) == | ||
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| 6 | The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software: | ||
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| 8 | 1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation. | ||
| 9 | 1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) enables nonlinear adjustments of the reference atlas to the experimental section. | ||
| 10 | 1. (% 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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| 12 | 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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| 14 | [[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]] | ||
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| 25 | ==== ==== | ||
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| 31 | ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==== | ||
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| 33 | * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge. | ||
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| 35 | ((( | ||
| 36 | * 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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| 38 | ==== (% style="color:#c0392b" %)**References**(%%) ==== | ||
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| 40 | 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 | ||
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| 42 | [[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]] | ||
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| 44 | [[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]] | ||
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| 46 | [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] | ||
| 47 | ))) |