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Last modified by puchades on 2022/11/02 10:16
From version 36.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version
To version 32.3
edited by puchades
on 2020/03/12 16:56
Change comment: There is no comment for this version

Summary

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1 1  (% style="text-align:center" %)
2 -[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
2 +[[image:QUINT_workflow_pic.png]]
3 3  
4 4  == (% style="color:#c0392b" %)**Workflow Description**(%%) ==
5 5  
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6 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:
7 7  
8 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//.
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.
11 11  
12 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.
13 13  
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31 31  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
32 32  
33 33  * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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45 45  
46 46  [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
47 47  )))
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