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Last modified by puchades on 2022/11/02 10:16
From version 19.1
edited by sharoncy
on 2020/03/09 14:11
Change comment: There is no comment for this version
To version 24.1
edited by sharoncy
on 2020/03/09 14:34
Change comment: There is no comment for this version

Summary

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15 15  
16 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.
18 +1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
19 +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.
20 +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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22 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]]
24 +[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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26 -
27 27  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
28 28  
29 -- The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
28 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
30 30  
31 31  (((
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.
31 +* 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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34 -
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