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Last modified by puchades on 2022/11/02 10:16
From version 4.1
edited by sharoncy
on 2020/03/09 13:03
Change comment: There is no comment for this version
To version 28.2
edited by puchades
on 2020/03/12 16:50
Change comment: There is no comment for this version

Summary

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1 -XWiki.sharoncy
1 +XWiki.puchades
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1 -(% class="jumbotron" %)
2 -(((
3 -(% class="container" %)
4 -(((
5 -= My Collab's Extended Title =
1 +(% style="text-align:center" %)
2 +[[image:QUINT_workflow_pic.png]]
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7 -My collab's subtitle
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15 -= What can I find here? =
5 +==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
7 +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:
20 20  
21 -= Who has access? =
9 +1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
10 +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.
11 +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.
22 22  
23 -Describe the audience of this collab.
24 -)))
13 +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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15 +[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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17 +==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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19 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
20 +
28 28  (((
29 -{{box title="**Contents**"}}
30 -{{toc/}}
31 -{{/box}}
22 +* 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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24 +==== (% style="color:#c0392b" %)**References**(%%) ====
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26 +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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28 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
29 +
30 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
31 +
32 +[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
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QUINT_workflow_pic.png
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