Changes for page QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain
Last modified by puchades on 2022/11/02 10:16
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... ... @@ -1,34 +1,35 @@ 1 -(% style="text-align:center" %) 2 -[[image:QUINT_workflow_pic.png]] 1 +(% class="jumbotron" %) 2 +((( 3 +(% class="container" %) 4 +((( 5 += My Collab's Extended Title = 3 3 7 +My collab's subtitle 8 +))) 9 +))) 4 4 5 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ==== 11 +(% class="row" %) 12 +((( 13 +(% class="col-xs-12 col-sm-8" %) 14 +((( 15 += What can I find here? = 6 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: 17 +* Notice how the table of contents on the right 18 +* is automatically updated 19 +* to hold this page's headers 8 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. 21 += Who has access? = 12 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. 23 +Describe the audience of this collab. 24 +))) 14 14 15 -[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]] 16 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. 20 - 27 +(% class="col-xs-12 col-sm-4" %) 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. 29 +{{box title="**Contents**"}} 30 +{{toc/}} 31 +{{/box}} 23 23 24 -==== (% style="color:#c0392b" %)**References**(%%) ==== 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 27 - 28 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]] 29 - 30 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]] 31 - 32 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] 33 + 33 33 ))) 34 - 35 +)))
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