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  • Illustration seg_flat_files.png

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10	10
11	11	It requires the following input:
12	12
13		-1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
	13	+1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14	14
15	15	**Requirement:**
16	16
17		-* must be 24-bit RGB images in PNG format.
18		-* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size).
	17	+* Input format: 24-bit RGB images in PNG
	18	+* The images have to have the same aspect ratio as the images used in QuickNII to generate the atlas maps (can be a different size).
19	19	* //Quantifier** **//is only able to extract one RGB colour at a time. Apply one RBG colour to all of the objects of interest, and specify this colour co//d//e in the GUI (e.g. 255, 0, 0 for red).
20	20
21	21	To generate the segmentations we recommend the //Pixel and// //Object Classification workflows// in the //ilastik// software (//ilastik.org//). However, any image analysis software may be used.
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28	28	(% start="3" %)
29	29	1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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31		-[[image:Illustration seg_flat_files.png||height="254" width="500"]]
	31	+[[image:Illustration seg_flat_files.png]]
32	32
33	33	== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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37	37
38	38	- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
39	39
40		-- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.
	40	+- Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.

Illustration seg_flat_files.png

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	1	+XWiki.puchades

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