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  • Quint tutorial video pic.png

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1		-XWiki.evanhancock
	1	+XWiki.puchades

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1		-[[image:QUINT_workflow_Plaques.png||style="float:left"]]
	1	+(% class="box infomessage" %)
	2	+(((
	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. ====
	4	+)))
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	6	+[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
	7	+
	8	+== ==
	9	+
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	20	+== ==
	21	+
	22	+== ==
	23	+
	24	+== ==
	25	+
	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]]
	34	+
	35	+[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]
	36	+
	37	+== ==
	38	+
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. **
	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. **
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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.**
	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.**
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9		-The workflow is built on the following open access software:
	45	+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.
	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.
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..
	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.
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.
	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.
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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]]
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	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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34	34	QUINT workflow video
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	81	+
36	36	== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
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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.
	86	+The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
41	41	)))
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43	43	(((
44	44	(% class="box successmessage" %)
45	45	(((
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.
	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.
47	47	)))
48	48
49	49	==== (% style="color:#c0392b" %)**References**(%%) ====

Quint tutorial video pic.png

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	1	+XWiki.puchades

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