Last modified by puchades on 2022/11/02 10:16
From version 72.2
edited by puchades
on 2022/02/07 13:12
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To version 36.1
edited by sharoncy
on 2020/03/30 17:18
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3 -==== This collab is describing the use of the software toolchain version of the QUINT workflow. The integrated QUINT service will soon be available here. ====
4 -)))
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2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
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6 -[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
7 7  
8 -== ==
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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10 -== ==
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 -== ==
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.
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14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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27 -==== Online documentation ====
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29 -[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
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31 -[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
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33 -[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
25 +==== ====
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35 -[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]                                  
36 36  
37 -== ==
38 38  
39 -== (% style="color:#c0392b" %)**Description**(%%) ==
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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. **
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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.**
31 +==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
44 44  
45 -The workflow is built on the following open-access software.
33 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
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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.
48 -* [[(% 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.
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.
50 -* (% 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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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.
51 51  
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.
38 +==== (% style="color:#c0392b" %)**References**(%%) ====
53 53  
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
54 54  
55 -[[[[image:Youtube_QUINT.PNG||height="310" style="float:right" width="550"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
42 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
56 56  
57 -[[[[image:Quint tutorial video pic.png||height="339" style="float:left" width="550"]]>>https://www.youtube.com/watch?v=n-gQigcGMJ0]]
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
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79 -QUINT workflow video
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81 -
82 -== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
83 -
84 -(% class="box successmessage" %)
85 -(((
86 -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/]]
87 87  )))
88 -
89 -(((
90 -(% class="box successmessage" %)
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 -)))
94 -
95 -==== (% style="color:#c0392b" %)**References**(%%) ====
96 -
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]]
98 -* 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]]
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]]
100 -* (((
101 -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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103 -
104 -==== ====
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