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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
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To version 20.1
edited by sharoncy
on 2020/03/09 14:11
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2 -[[image:QUINT_workflow_pic.png]]
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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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4 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
7 +(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
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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:
11 +==== ====
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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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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.
14 +==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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14 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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:
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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.
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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.
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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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28 28  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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30 30  * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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32 32  (((
33 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.
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35 35  ==== (% style="color:#c0392b" %)**References**(%%) ====
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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
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39 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
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/]]
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41 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
41 +[[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
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43 43  [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
44 44  )))
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