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1	1	== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2	2
3		-A detailed Nutil user manual is included when downloading the software.
	3	+A detailed user manual is included when downloading the software.
4	4
5	5	[[image:Quantifier.PNG]]
6	6
7	7	**Basic steps:**
8	8
9		-**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
	9	+**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
10	10
11		-(% start="1" style="list-style-type:decimal" %)
12		-1. **Segmentations with the labeling displayed in one RGB colour**
	11	+It requires the following input:
13	13
	13	+1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
	14	+
14	14	**Requirement:**
15	15
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//.
	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).
19	19
20	20	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.
21	21
22	22	(% start="2" %)
23		-1. **Customised anatomical atlas maps**
	24	+1. (% style="color:#c0392b" %)**Customised atlas maps**
24	24
25		-Generate the atlas maps in FLAT format with the //QuickNII //software
	26	+Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
26	26
27	27	(% start="3" %)
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).
	29	+1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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	+
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