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1		-== (% style="color:#c0392b" %)//Nutil Quantifier//(%%) ==
	1	+== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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3		-A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
	3	+A detailed user manual is included when downloading the software.
4	4
5	5	[[image:Nutil_GUI.png||style="float:left"]]
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	34	+**Basic steps:**
34	34
	36	+**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
35	35
36		-**Basic steps**
	38	+It requires the following input:
37	37
38		-//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
39		-
40		-It requires the following input.
41		-
42	42	1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
43	43
44		-**Requirement**
	42	+**Requirement:**
45	45
46		-* Input format: 24-bit RGB images in PNG.
47		-* 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).
48		-* //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 GUI (e.g., 255, 0, 0 for red).
	44	+* Input format: 24-bit RGB images in PNG
	45	+* 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).
	46	+* //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).
49	49
50		-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.
	48	+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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52	52	(% start="2" %)
53	53	1. (% style="color:#c0392b" %)**Customised atlas maps**
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55		-Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
	53	+Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
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57	57	(% start="3" %)
58	58	1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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62	62	== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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64	64
65		-The //Nutil //software is currently compatible with
	63	+The Nutil software is currently compatible with:
66	66
67		-* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
	65	+* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
68	68	* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.