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1		-XWiki.puchades
	1	+XWiki.annedevismes

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36		-**Basic steps:**
	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).
	38	+//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
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40		-It requires the following input:
	40	+It requires the following input.
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42	42	1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
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44		-**Requirement:**
	44	+**Requirement**
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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 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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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.
	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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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//).
	55	+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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65		-The Nutil software is currently compatible with:
	65	+The //Nutil //software is currently compatible with
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67		-* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
	67	+* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
68	68	* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.