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Author

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1		-XWiki.evanhancock
	1	+XWiki.annedevismes

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3	3	== (% style="color:#c0392b" %)**Description**(%%) ==
4	4
5		-**The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
	5	+**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
6	6
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.**
	7	+**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.**
8	8
9		-The workflow is built on the following open access software:
	9	+The workflow is built on the following open-access software.
10	10
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.
	11	+* [[(% 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.
12	12	* [[(% 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.
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..
	13	+* //[[(% 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.
14	14	* (% 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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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.
	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	18	[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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38	38	(% class="box successmessage" %)
39	39	(((
40		-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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43	43	(((
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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.
	46	+Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
47	47	)))
48	48
49	49	==== (% style="color:#c0392b" %)**References**(%%) ====