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1	1	(% class="box infomessage" %)
2	2	(((
3		-==== Online documentation ====
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]]
	3	+==== This collab describes the use of the desktop version of the QUINT workflow. The integrated QUINT online service will soon be available [[here.>>https://wiki.ebrains.eu/bin/edit/Collabs/quint-demo/WebHome]] ====
12	12	)))
13	13
14		-
15	15	[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
16	16
17	17	== ==
...	...	@@ -26,36 +26,47 @@
26	26
27	27	== ==
28	28
29		-== (% style="color:#c0392b" %)**Description**(%%) ==
	20	+== ==
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. **
	22	+== ==
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.**
	24	+== ==
34	34
35		-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.
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.
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//.
	27	+==== Online documentation ====
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.
	29	+[[QUINT workflow user documentation>>https://quint-workflow.readthedocs.io]]
43	43
	31	+[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
44	44
45		-[[[[image:Youtube_QUINT.PNG||height="310" style="float:right" width="550"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
	33	+[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
46	46
47		-[[[[image:Quint tutorial video pic.png||height="339" style="float:left" width="550"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
	35	+[[Ilastik user documentation>>https://quint-workflow.readthedocs.io]]
48	48
	37	+[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]
49	49
	39	+[[MeshView user documentation>>https://meshview-for-brain-atlases.readthedocs.io]]
50	50
	41	+== ==
51	51
	43	+== (% style="color:#c0392b" %)**Description**(%%) ==
52	52
	45	+**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
53	53
	47	+**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.**
54	54
	49	+The workflow is built on the following open-access software.
55	55
	51	+* [[(% 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.
	52	+* [[(% 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.
	53	+* //[[(% 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.
	54	+* (% 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//.
56	56
	56	+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.
57	57
	58	+[[[[image:Youtube_QUINT.PNG||height="281" style="float:right" width="499"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
58	58
	60	+[[[[image:Quint tutorial video pic.png||height="300" style="float:left" width="487"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
59	59
60	60
61	61
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66	66
67	67
68	68
	71	+
69	69	QUINT workflow video
70	70
71	71

Collaboratory.Apps.Collab.Code.CollabClass[0]

owner

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	1	+sharoncy