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Last modified by puchades on 2022/11/02 10:16
From version 26.1
edited by sharoncy
on 2020/03/09 14:37
Change comment: There is no comment for this version
To version 23.1
edited by sharoncy
on 2020/03/09 14:30
Change comment: There is no comment for this version

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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:
17 17  
18 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.
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  
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34 34  
35 35  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
36 36  
37 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
37 +[[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/]]
38 38  
39 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
39 +[[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]
40 40  
41 41  [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
42 42  )))