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Last modified by puchades on 2022/11/02 10:16
From version 54.1
edited by puchades
on 2020/09/24 11:41
Change comment: There is no comment for this version
To version 76.1
edited by sharoncy
on 2022/02/11 11:24
Change comment: There is no comment for this version

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1 -[[image:QUINT_workflow_Plaques.png||style="float:left"]]
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2 +(((
3 +==== This collab is describing 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  
6 +[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
7 +
8 +== ==
9 +
10 +== ==
11 +
12 +== ==
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14 +== ==
15 +
16 +== ==
17 +
18 +== ==
19 +
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. **
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.**
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.**
8 8  
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//.
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.
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.
17 17  
18 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
19 19  
55 +[[[[image:Youtube_QUINT.PNG||height="281" style="float:right" width="499"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
20 20  
57 +[[[[image:Quint tutorial video pic.png||height="300" style="float:left" width="487"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
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34 34  QUINT workflow video
35 35  
81 +
36 36  == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
37 37  
38 -* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
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85 +(((
86 +The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
87 +)))
39 39  
40 40  (((
41 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
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91 +(((
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.
93 +)))
42 42  
43 43  ==== (% style="color:#c0392b" %)**References**(%%) ====
44 44  
45 -* Yates SC et al. 2019. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
97 +* Yates SC et al. (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
46 46  * Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
47 -* Berg S, Kutra D, Kroeger T, et al. & Kreshuk A (2019) ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 16:1226-1232. doi: [[10.1038/s41592-019-0582-9>>attach:https://www.nature.com/articles/s41592-019-0582-9]]
99 +* Berg S, Kutra D, Kroeger T, et al. & Kreshuk A (2019) ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 16:1226-1232. doi: [[10.1038/s41592-019-0582-9>>https://www.nature.com/articles/s41592-019-0582-9]]
48 48  * (((
49 49  Puchades MA et al. (2019) Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PlosOne. 14(5): e0216796. doi: [[10.1371/journal.pone.0216796>>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216796]]
50 50  )))
51 51  
52 -==== (% style="color:#c0392b" %)**User support**(%%) ====
53 -
54 -* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
55 -* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
56 -* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
57 -* [[ilastik>>https://www.ilastik.org/]]
104 +==== ====
58 58  )))
Quint tutorial video pic.png
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