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Last modified by puchades on 2022/11/02 10:16
From version 61.1
edited by evanhancock
on 2021/04/16 21:27
Change comment: There is no comment for this version
To version 82.1
edited by puchades
on 2022/09/23 09:38
Change comment: There is no comment for this version

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1 -[[image:QUINT_workflow_Plaques.png||style="float:left"]]
1 +(% class="box infomessage" %)
2 +(((
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]] ====
4 +)))
2 2  
3 -== (% style="color:#c0392b" %)**Description**(%%) ==
6 +[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
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. **
8 +== ==
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.**
10 +== ==
8 8  
9 -The workflow is built on the following open access software:
12 +== ==
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.
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..
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//.
14 +== ==
15 15  
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 +== ==
17 17  
18 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
18 +== ==
19 19  
20 +== ==
20 20  
22 +== ==
21 21  
24 +== ==
22 22  
23 23  
27 +==== Online documentation ====
24 24  
29 +[[QUINT workflow user documentation>>https://quint-workflow.readthedocs.io]]
25 25  
31 +[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
26 26  
33 +[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
27 27  
35 +[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
28 28  
37 +[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]] 
29 29  
39 +[[MeshView user documentation>>https://meshview-for-brain-atlases.readthedocs.io]]                               
30 30  
41 +== ==
31 31  
43 +== (% style="color:#c0392b" %)**Description**(%%) ==
32 32  
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. **
33 33  
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.**
48 +
49 +The workflow is built on the following open-access software.
50 +
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//.
55 +
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 +
58 +[[[[image:Youtube_QUINT.PNG||height="281" style="float:right" width="499"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
59 +
60 +[[[[image:Quint tutorial video pic.png||height="300" style="float:left" width="487"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
61 +
62 +
63 +
64 +
65 +
66 +
67 +
68 +
69 +
70 +
71 +
34 34  QUINT workflow video
35 35  
74 +
36 36  == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
37 37  
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.
79 +The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
41 41  )))
42 42  
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.
85 +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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