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Last modified by puchades on 2022/11/02 10:16
From version 20.1
edited by sharoncy
on 2020/03/09 14:11
Change comment: There is no comment for this version
To version 35.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version

Summary

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2 -(((
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4 -(((
5 -== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
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2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
6 6  
7 -(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
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4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
10 10  
11 -==== ====
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//.
13 13  
14 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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.
15 15  
16 -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:
14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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18 -1. (% style="color:#2980b9" %)//ilastik//(%%) allows the extraction of labelled features such as cells by segmentation.
19 -1. (% style="color:#2980b9" %)//QuickNII//(%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections.
20 -1. (% style="color:#2980b9" %)//Nutil//(%%) enables image transformations, in addition to quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.
21 21  
22 -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.
23 23  
24 -Youtube video:[[ https:~~/~~/www.youtube.com/watch?v=yPkAbSfla_c>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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25 +==== ====
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27 27  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
28 28  
29 29  * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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31 31  (((
32 32  * 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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35 35  ==== (% style="color:#c0392b" %)**References**(%%) ====
36 36  
37 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
38 38  
39 -[[https>>url:https://www.nitrc.org/projects/nutil/]][[:~~/~~/www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/nutil/]]
42 +[[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:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
42 42  
43 43  [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
44 44  )))
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