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Last modified by puchades on 2022/11/02 10:16
From version 73.1
edited by puchades
on 2022/02/07 13:12
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To version 61.1
edited by evanhancock
on 2021/04/16 21:27
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3 -==== This collab is describing the use of the software toolchain version of the QUINT workflow. The integrated QUINT service will soon be available [[here.>>https://wiki.ebrains.eu/bin/edit/Collabs/quint-demo/WebHome]] ====
4 -)))
1 +[[image:QUINT_workflow_Plaques.png||style="float:left"]]
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6 -[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
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26 -
27 -==== Online documentation ====
28 -
29 -[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
30 -
31 -[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
32 -
33 -[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
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35 -[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]                                  
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37 -== ==
38 -
39 39  == (% style="color:#c0392b" %)**Description**(%%) ==
40 40  
41 -**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
5 +**The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
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43 -**Examples of use are cell counting and spatial distributions, determination of projection areas in connectivity experiments, and exploration of pathological hallmarks in brain-disease models. Integration of various data to the same reference space enables new exploration strategies and reuse of experimental data.**
7 +**Examples of use are: cell counting and spatial distributions; determination of projection areas in connectivity experiments; exploration of pathological hallmarks in brain disease models. Integration of various data to the same reference space enables new exploration strategies and re-use of experimental data.**
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45 -The workflow is built on the following open-access software.
9 +The workflow is built on the following open access software:
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47 -* [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells, by using machine-learning image segmentation.
11 +* [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells, using machine learning image segmentation.
48 48  * [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates custom-angle slices from volumetric brain atlases to match the proportions and cutting plane of histological sections.
49 -* //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) is then used for non-linear alignment of the reference-atlas slice to the section image.
13 +* //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) is then used for nonlinear alignment of the reference atlas slice to the section image..
50 50  * (% 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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52 -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.
16 +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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18 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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55 -[[[[image:Youtube_QUINT.PNG||height="310" style="float:right" width="550"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
56 56  
57 -[[[[image:Quint tutorial video pic.png||height="339" style="float:left" width="550"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
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79 79  QUINT workflow video
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81 -
82 82  == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
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86 -The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
40 +The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
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92 -Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
46 +As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
93 93  )))
94 94  
95 95  ==== (% style="color:#c0392b" %)**References**(%%) ====
Quint tutorial video pic.png
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