Summary

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Author

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1		-XWiki.annedevismes
	1	+XWiki.puchades

Content

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3	3
4	4	1. (% style="color:#c0392b" %)**Images in PNG format**
5	5
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.
	6	+Segmentations superimposed on the atlas maps. Object colours are assigned based on the sheet specified under “Report Regions”. If custom areas and colours are not specified, or object falls outside of the specified areas, the objects are shown in red by default.
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8	8	[[image:0209_71661877_resize_Simple Segmentation.png]]
9	9
10		-(% class="small" %)Customised atlas map with individual features representation
	10	+(% class="small" %)Customized atlas map with individual features representation
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12	12
13	13	(% start="2" %)
14	14	1. (% style="color:#c0392b" %)**Reports in CSV format**
15	15
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.
	16	+* RefAtlasRegions: report with output organised based on all the regions in the reference atlas.
	17	+* CustomRegionsSummary and CustomRegionSections**: **reports with the output organised based on 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 whole series (Whole Brain), with sheets showing breakdown per section.
19	19
20	20	[[image:Report_example.PNG]]
21	21
22	22	(% start="3" %)
23		-1. (% style="color:#c0392b" %)**Coordinates in JSON format (for the entire series and per section)**
	23	+1. (% style="color:#c0392b" %)**Coordinates in JSON format (for the whole series and per section)**
24	24
25		-* The JSON files contain point cloud coordinates in the selected reference-atlas space that can be visualised with the //MeshView //atlas viewer.
	25	+* The JSON files contains point clouds coordinates in the selected reference atlas space that can be visualised with the MeshView atlas viewer.
26	26
27		-== (% style="color:#c0392b" %)Visualise the //QUINT //output(%%) ==
	27	+== (% style="color:#c0392b" %)Visualise the QUINT output(%%) ==
28	28
29	29
30	30	[[image:QUINTpoint cloud.png]]
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32	32
33		-(% 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.
	33	+Point clouds visualised with MeshView.