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Last modified by puchades on 2022/11/02 10:16
From version 64.1
edited by sharoncy
on 2021/10/18 09:39
Change comment: There is no comment for this version
To version 35.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version

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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]]                                                                                        
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2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
5 5  
6 -Please, address your questions about our tools and workflows to [[https:~~/~~/ebrains.eu/support/>>https://ebrains.eu/support/]].
4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
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8 -[[image:User_support_Ebrains.png]]
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:
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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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11 -[[image:QUINT_workflow_Plaques.png||style="float:left"]]
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.
12 12  
13 -== (% style="color:#c0392b" %)**Description**(%%) ==
14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
14 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. **
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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 18  
19 -The workflow is built on the following open-access software.
20 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.
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//.
25 25  
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.
27 27  
28 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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25 +==== ====
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37 37  
31 +==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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33 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
39 39  
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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.
40 40  
38 +==== (% style="color:#c0392b" %)**References**(%%) ====
41 41  
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
42 42  
42 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
43 43  
44 -QUINT workflow video
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
45 45  
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.
46 +[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
51 51  )))
52 -
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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 -)))
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]]
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68 -==== ====
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QUINT_workflow_Plaques.png
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