Last modified by puchades on 2022/11/02 10:16
From version 10.1
edited by sharoncy
on 2020/03/09 14:03
Change comment: There is no comment for this version
To version 13.1
edited by sharoncy
on 2020/03/09 14:04
Change comment: There is no comment for this version

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11 11  ==== ====
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14 -==== (% style="color:#c0392b" %)Workflow Description(%%) ====
14 +==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
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. ilastik allows the extraction of labelled features such as cells by segmentation.
19 -1. QuickNII generates atlas maps customised to match the proportions and cutting plane of the brain sections.
20 -1. 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//(%%) 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 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