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28.2 | 1 | (% style="text-align:center" %) |
| 2 | [[image:QUINT_workflow_pic.png]] | ||
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7.1 | 3 | |
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30.2 | 4 | == (% style="color:#c0392b" %)**Workflow Description**(%%) == |
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8.1 | 5 | |
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9.1 | 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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23.1 | 8 | 1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation. |
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24.1 | 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. |
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27.1 | 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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9.1 | 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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30.2 | 14 | [[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]] |
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14.1 | 40 | ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==== |
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20.1 | 42 | * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge. |
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20.1 | 45 | * 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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| 47 | ==== (% style="color:#c0392b" %)**References**(%%) ==== | ||
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| 49 | 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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25.1 | 51 | [[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]] |
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15.1 | 52 | |
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26.1 | 53 | [[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]] |
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15.1 | 54 | |
| 55 | [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] | ||
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14.1 | 56 | ))) |
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30.2 | 58 |