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Last modified by puchades on 2022/11/02 10:16
From version 71.1
edited by puchades
on 2021/12/07 10:30
Change comment: There is no comment for this version
To version 62.1
edited by evanhancock
on 2021/04/16 21:27
Change comment: There is no comment for this version

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2 -(((
3 -==== Online documentation ====
1 +[[image:QUINT_workflow_Plaques.png||style="float:left"]]
4 4  
5 -[[QuickNII user documentation>>https://quicknii.readthedocs.io/en/latest/index.html]]
6 -
7 -[[VisuAlign user documentation>>https://visualign.readthedocs.io/en/latest/index.html]]
8 -
9 -[[Ilastik user documentation>>https://nutil.readthedocs.io/en/latest/Ilastik.html]]
10 -
11 -[[Nutil user documentation>>https://nutil.readthedocs.io/en/latest/index.html]]                                                                   
12 -)))
13 -
14 -
15 -[[image:QUINT_workflow_Plaques.png||height="470" style="float:left" width="1277"]]
16 -
17 -== ==
18 -
19 -== ==
20 -
21 -== ==
22 -
23 -== ==
24 -
25 -== ==
26 -
27 -== ==
28 -
29 29  == (% style="color:#c0392b" %)**Description**(%%) ==
30 30  
31 -**The QUINT workflow enables an atlas-based analysis of extracted features from histological image sections from the rodent brain by using 3D reference atlases. **
5 +**The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
32 32  
33 -**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.**
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.**
34 34  
35 -The workflow is built on the following open-access software.
9 +The workflow is built on the following open access software:
36 36  
37 -* [[(% 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.
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.
38 38  * [[(% 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.
39 -* //[[(% 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.
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..
40 40  * (% 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//.
41 41  
42 -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.
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.
43 43  
44 -[[[[image:Youtube_QUINT.PNG||height="338" style="float:right" width="600"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
18 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
45 45  
46 -[[image:Quint tutorial video pic.png||height="370" style="float:left" width="600"]]
47 47  
48 48  
49 49  
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56 56  
57 57  
58 58  
32 +
33 +
59 59  QUINT workflow video
60 60  
61 61  == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
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62 62  
63 63  (% class="box successmessage" %)
64 64  (((
65 -The semi-automated QUINT workflow uses open-access software that can be operated without any scripting knowledge.
40 +The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
66 66  )))
67 67  
68 68  (((
69 69  (% class="box successmessage" %)
70 70  (((
71 -Because the quantifications are performed in regions defined by a reference atlas, the region definitions are standardised, allowing comparisons of data from different laboratories.
46 +As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
72 72  )))
73 73  
74 74  ==== (% style="color:#c0392b" %)**References**(%%) ====
Quint tutorial video pic.png
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