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1		-== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
	1	+== (% style="color:#c0392b" %)//Nutil Quantifier//(%%) ==
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3		-A detailed user manual is included when downloading the software.
	3	+A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
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5	5	[[image:Nutil_GUI.png||style="float:left"]]
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34		-**Basic steps:**
35	35
36		-**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
37	37
38		-It requires the following input:
	36	+**Basic steps**
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	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	+
40	40	1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
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42		-**Requirement:**
	44	+**Requirement**
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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).
	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).
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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.
	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.
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50	50	(% start="2" %)
51	51	1. (% style="color:#c0392b" %)**Customised atlas maps**
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53		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
	55	+Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
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55	55	(% start="3" %)
56	56	1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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60	60	== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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62	62
63		-The Nutil software is currently compatible with:
	65	+The //Nutil //software is currently compatible with
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65		-* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
66		-* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.
	67	+* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
	68	+* Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4.