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Last modified by puchades on 2022/11/02 10:16
From version 36.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version
To version 63.1
edited by puchades
on 2021/10/18 09:38
Change comment: There is no comment for this version

Summary

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2 -[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
1 +(% class="box infomessage" %)
2 +(((
3 +Online documentation: - [[https:~~/~~/quicknii.readthedocs.io/en/latest/index.html>>https://quicknii.readthedocs.io/en/latest/index.html]] [[-https:~~/~~/visualign.readthedocs.io/en/latest/index.html#>>https://visualign.readthedocs.io/en/latest/index.html#]][[ -https:~~/~~/nutil.readthedocs.io/en/latest/index.html>>https://nutil.readthedocs.io/en/latest/index.html]]
4 +)))
3 3  
4 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
6 +Please, address your questions about our tools and workflows to [[https:~~/~~/ebrains.eu/support/>>https://ebrains.eu/support/]].
5 5  
6 -The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software:
8 +[[image:User_support_Ebrains.png]]
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8 -1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
9 -1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) enables nonlinear adjustments of the reference atlas to the experimental section.
10 -1. (% 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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12 -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.
11 +[[image:QUINT_workflow_Plaques.png||style="float:left"]]
13 13  
14 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
13 +== (% style="color:#c0392b" %)**Description**(%%) ==
15 15  
15 +**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
16 16  
17 +**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.**
17 17  
19 +The workflow is built on the following open-access software.
18 18  
21 +* [[(% 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.
22 +* [[(% 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.
23 +* //[[(% 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.
24 +* (% 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//.
19 19  
26 +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.
20 20  
28 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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22 22  
23 23  
24 24  
25 -==== ====
26 26  
27 27  
28 28  
29 29  
30 30  
31 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
32 32  
33 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
34 34  
35 -(((
36 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
37 37  
38 -==== (% style="color:#c0392b" %)**References**(%%) ====
39 39  
40 -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
41 41  
42 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
43 43  
44 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
44 +QUINT workflow video
45 45  
46 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
46 +== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
47 +
48 +(% class="box successmessage" %)
49 +(((
50 +The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
47 47  )))
52 +
53 +(((
54 +(% class="box successmessage" %)
55 +(((
56 +Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
57 +)))
58 +
59 +==== (% style="color:#c0392b" %)**References**(%%) ====
60 +
61 +* 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]]
62 +* 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]]
63 +* 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]]
64 +* (((
65 +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]]
66 +)))
67 +
68 +==== ====
69 +)))
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