Last modified by puchades on 2022/11/02 10:16
From version 50.1
edited by puchades
on 2020/09/24 10:26
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To version 36.1
edited by sharoncy
on 2020/03/30 17:18
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1 -[[image:QUINT_workflow_Plaques.png||style="float:left"]]
1 +(% style="text-align:center" %)
2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
2 2  
3 -== (% style="color:#c0392b" %)**Description**(%%) ==
4 +== (% style="color:#c0392b" %)**Workflow 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. **
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:
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.**
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//.
8 8  
9 -The workflow is built on the following open access software:
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.
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..
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 -
16 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.
17 17  
18 18  [[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
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26 26  
27 27  
28 28  
25 +==== ====
29 29  
30 30  
31 31  
32 32  
33 33  
34 -QUINT workflow video
35 -
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.
33 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
39 39  
40 40  (((
41 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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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]]
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
47 -* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
48 -* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
49 -* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
50 -* [[ilastik>>https://www.ilastik.org/]]
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 +
42 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
43 +
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
45 +
46 +[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
51 51  )))
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