Last modified by puchades on 2022/02/18 13:42
From version 1.2
edited by puchades
on 2020/03/24 18:06
Change comment: There is no comment for this version
To version 18.1
edited by puchades
on 2021/11/16 08:12
Change comment: There is no comment for this version

Summary

Details

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1 -== H2 Headings Will Appear in Table of Content ==
1 +== (% style="color:#c0392b" %)How to interpret the //Nutil Quantifier// output(%%) ==
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3 3  
4 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
4 +1. (% style="color:#c0392b" %)**Images in PNG format**
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6 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
6 +Segmentations superimposed on the atlas maps. Object colours are assigned on the basis of the sheet specified under “Report Regions.” If custom areas and colours are not specified or the object falls outside of the specified areas, the objects are shown in red by default.
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8 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
8 +[[image:0209_71661877_resize_Simple Segmentation.png]]
9 9  
10 -=== H3 Headings Will Appear In The Table of Content ===
10 +(% class="small" %)Customised atlas map with individual features representation
11 11  
12 -==== You can also add images ====
13 13  
14 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
13 +(% start="2" %)
14 +1. (% style="color:#c0392b" %)**Reports in CSV format**
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16 -Photo by David Clode
16 +* RefAtlasRegions: report with output organised on the basis of all the regions in the reference atlas.
17 +* CustomRegionsSummary and CustomRegionSections:** **reports with the output organised on the basis of the custom regions defined in the template for the whole series (Summary) and for each individual section.
18 +* Objects: list of all the objects in the entire series (Whole Brain), with sheets showing breakdown per section.
17 17  
18 -==== Or code ====
20 +[[image:Report_example.PNG]]
19 19  
20 -Code blocks can be added by using the code macro:
22 +(% start="3" %)
23 +1. (% style="color:#c0392b" %)**Coordinates in JSON format (for the entire series and per section)**
21 21  
22 -{{code language="python"}}
23 -x = 1
24 -if x == 1:
25 - # indented four spaces
26 - print("x is 1.")
27 -{{/code}}
25 +* The JSON files contain point cloud coordinates in the selected reference-atlas space that can be visualised with the //MeshView //atlas viewer.
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29 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30 -
27 +== (% style="color:#c0392b" %)Visualise the //QUINT //output(%%) ==
28 +
29 +A manual for MeshView can be found [[here>>https://meshview-for-brain-atlases.readthedocs.io]].
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31 +[[image:QUINTpoint cloud.png]]
32 +
33 +
34 +(% class="small" %)Point clouds visualised with //MeshView//. Location of human amyloid in blue, mouse amyloid in red, and pyroglutamate modified amyloid in green, in Hippocampal regions of transgenic Tg2573 mouse brain. Yates et al. 2019.
0209_71661877_resize_Simple Segmentation.png
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QUINTpoint cloud.png
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Quantifier output.png
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Report_example.PNG
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