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Author

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1		-XWiki.sharoncy
	1	+XWiki.evanhancock

Content

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1		-(% class="box infomessage" %)
2		-(((
3		-==== Online documentation ====
	1	+[[image:QUINT_workflow_Plaques.png||style="float:left"]]
4	4
5		-[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
6		-
7		-[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
8		-
9		-[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
10		-
11		-[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]
12		-)))
13		-
14		-
15		-[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
16		-
17		-== ==
18		-
19		-== ==
20		-
21		-== ==
22		-
23		-== ==
24		-
25		-== ==
26		-
27		-== ==
28		-
29	29	== (% style="color:#c0392b" %)**Description**(%%) ==
30	30
31		-**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. **
32	32
33		-**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.**
34	34
35		-The workflow is built on the following open-access software.
	9	+The workflow is built on the following open access software:
36	36
37		-* [[(% 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.
38	38	* [[(% 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.
39		-* //[[(% 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..
40	40	* (% 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//.
41	41
42		-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.
43	43
44	44	[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
45	45
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63	63
64	64	(% class="box successmessage" %)
65	65	(((
66		-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.
67	67	)))
68	68
69	69	(((
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72		-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.
73	73	)))
74	74
75	75	==== (% style="color:#c0392b" %)**References**(%%) ====