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1	1	== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2	2
3		-A detailed user manual is included when downloading the software.
	3	+A detailed Nutil user manual is included when downloading the software.
4	4
5	5	[[image:Quantifier.PNG]]
6	6
7	7	**Basic steps:**
8	8
9		-**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
	9	+**//Nutil Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
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 labeling displayed in one RGB colour**
14	14
15	15	**Requirement:**
16	16
17	17	* must be 24-bit RGB images in PNG format.
18	18	* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size).
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).
	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 code in the //Excel template//.
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.
22	22
23	23	(% start="2" %)
24		-1. (% style="color:#c0392b" %)**Customised atlas maps**
	24	+1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
25	25
26		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
	26	+Generate the atlas maps in FLAT format with the //QuickNII //software.
27	27
28	28	(% start="3" %)
29	29	1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	30	+1. (% style="color:#c0392b" %)**Reference atlas label file**(%%) (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the //Nutil// package (in the “Labels” folder).
30	30
31	31	[[image:Illustration seg_flat_files.png||height="254" width="500"]]
32	32
33	33
34		-== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35		-
36		-
37		-The Nutil software is currently compatible with:
38		-
39		-- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40		-
41		-- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.
42		-
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Quantifier.PNG

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