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Last modified by puchades on 2022/11/02 10:16
From version 40.1
edited by evanhancock
on 2020/07/28 18:04
Change comment: There is no comment for this version
To version 50.1
edited by puchades
on 2020/09/24 10:26
Change comment: There is no comment for this version

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2 -[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
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3 3  
4 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
3 +== (% style="color:#c0392b" %)**Description**(%%) ==
5 5  
6 -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:
5 +**The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
7 7  
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 +
9 +The workflow is built on the following open access software:
10 +
8 8  * [[(% 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.
9 9  * [[(% 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.
10 10  * //[[(% 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..
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25 25  
26 -==== ====
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34 +QUINT workflow video
35 +
32 32  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
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34 34  * The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
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39 39  ==== (% style="color:#c0392b" %)**References**(%%) ====
40 40  
41 41  * 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]]
42 -* [[Nutil>>https://www.nitrc.org/projects/nutil/]]
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]]
43 43  * [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
44 44  * [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
45 45  * [[ilastik>>https://www.ilastik.org/]]
QUINT_workflow_Plaques.png
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