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Last modified by puchades on 2022/11/02 10:16
From version 28.2
edited by puchades
on 2020/03/12 16:50
Change comment: There is no comment for this version
To version 8.1
edited by sharoncy
on 2020/03/09 13:53
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  
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4 +(((
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6 +(((
7 +== QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain ==
8 +)))
9 +)))
4 4  
5 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
6 -
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:
8 -
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.
12 -
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.
14 -
15 -[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
16 -
17 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
18 -
19 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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21 21  (((
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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23 23  
24 -==== (% style="color:#c0392b" %)**References**(%%) ====
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19 +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. The first – ilastik - allows the extraction of labelled features such as cells by segmentation. The second – QuickNII - generates atlas maps customised to match the proportions and cutting plane of the brain sections. The third – Nutil – enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII. 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.
25 25  
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
21 += What can I find here? =
27 27  
28 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
23 +* Notice how the table of contents on the right
24 +* is automatically updated
25 +* to hold this page's headers
29 29  
30 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
27 += Who has access? =
31 31  
32 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
29 +Describe the audience of this collab.
33 33  )))
34 -
31 +)))
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