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Last modified by puchades on 2022/11/02 10:16
From version 32.1
edited by puchades
on 2020/03/12 16:56
Change comment: There is no comment for this version
To version 6.1
edited by sharoncy
on 2020/03/09 13:15
Change comment: There is no comment for this version

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2 -[[image:QUINT_workflow_pic.png]]
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3 3  
4 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
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7 +== QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain ==
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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.
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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17 += What can I find here? =
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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.
19 +* Notice how the table of contents on the right
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14 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
23 += Who has access? =
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25 +Describe the audience of this collab.
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25 -==== ====
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28 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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30 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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33 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
31 +{{box title="**Contents**"}}
32 +{{toc/}}
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35 -==== (% style="color:#c0392b" %)**References**(%%) ====
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37 -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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39 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
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41 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
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43 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
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