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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	+**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
10	10
11		-It requires the following input:
	11	+(% start="1" style="list-style-type:decimal" %)
	12	+1. **Segmentations with the labeling displayed in one RGB colour**
12	12
13		-1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
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).
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).
	16	+* must be 24-bit RGB images in PNG format
	17	+* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
	18	+* //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**
	23	+1. **Customised anatomical atlas maps**
25	25
26		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
	25	+Generate the atlas maps in FLAT format with the //QuickNII //software
27	27
28	28	(% start="3" %)
29		-1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	28	+1. **Anchored XML** file generated with the //QuickNII// software.
	29	+1. **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"]]
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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		-
	34	+

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