Last modified by puchades on 2022/11/02 10:16
From version 27.2
edited by puchades
on 2020/03/12 16:34
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To version 9.1
edited by sharoncy
on 2020/03/09 14:01
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7 +== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
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9 +(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
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1 1  ==== ====
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4 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
16 +==== (% style="color:#c0392b" %)Workflow Description(%%) ====
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6 6  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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8 -1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
9 -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.
10 -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.
20 +1. ilastik allows the extraction of labelled features such as cells by segmentation.
21 +1. QuickNII generates atlas maps customised to match the proportions and cutting plane of the brain sections.
22 +1. Nutil enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.
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12 12  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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14 -[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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16 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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18 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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21 -* 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 -==== (% style="color:#c0392b" %)**References**(%%) ====
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25 -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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27 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
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29 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
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31 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
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