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Last modified by puchades on 2022/11/02 10:16
From version 47.1
edited by puchades
on 2020/09/24 09:55
Change comment: Uploaded new attachment "QUINT_workflow_Plaques.png", version {1}
To version 63.1
edited by puchades
on 2021/10/18 09:38
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Summary

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2 -[[image:QUINT_workflow_pic.png||height="391" width="1003"]]
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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  
6 +Please, address your questions about our tools and workflows to [[https:~~/~~/ebrains.eu/support/>>https://ebrains.eu/support/]].
4 4  
5 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
8 +[[image:User_support_Ebrains.png]]
6 6  
7 -The QUINT workflow facilitates the quantification and spatial analysis of labelled features in images of histological sections from the rodent brain using 3D reference atlases. The workflow is built on the following open access software:
8 8  
9 -* [[(% 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.
11 +[[image:QUINT_workflow_Plaques.png||style="float:left"]]
12 +
13 +== (% style="color:#c0392b" %)**Description**(%%) ==
14 +
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 +
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.**
18 +
19 +The workflow is built on the following open-access software.
20 +
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.
10 10  * [[(% 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.
11 -* //[[(% 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..
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.
12 12  * (% 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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14 -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.
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.
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16 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
28 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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31 31  
32 32  QUINT workflow video
33 33  
34 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
46 +== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
35 35  
36 -* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
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49 +(((
50 +The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
51 +)))
37 37  
38 38  (((
39 -* 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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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 +)))
40 40  
41 41  ==== (% style="color:#c0392b" %)**References**(%%) ====
42 42  
43 -* 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]]
44 -* 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
45 -* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
46 -* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
47 -* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
48 -* [[ilastik>>https://www.ilastik.org/]]
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]]
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68 +==== ====
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