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1		-== Nutil Quantifier ==
	1	+== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2	2
3		-A detailed Nutil user manual
	3	+A detailed user manual is included when downloading the software.
4	4
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	5	+[[image:Nutil_main.PNG]]
6	6
7		->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
	7	+**Basic steps:**
8	8
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	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		-=== H3 Headings Will Appear In The Table of Content ===
	11	+It requires the following input:
12	12
13		-==== You can also add images ====
	13	+1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14	14
15		-[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
	15	+**Requirement:**
16	16
17		-Photo by David Clode
	17	+* Input format: 24-bit RGB images in PNG
	18	+* 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).
	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).
18	18
19		-==== Or code ====
	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.
20	20
21		-Code blocks can be added by using the code macro:
	23	+(% start="2" %)
	24	+1. (% style="color:#c0392b" %)**Customised atlas maps**
22	22
23		-{{code language="python"}}
24		-x = 1
25		-if x == 1:
26		- # indented four spaces
27		- print("x is 1.")
28		-{{/code}}
	26	+Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
29	29
30		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
31		-
	28	+(% start="3" %)
	29	+1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	30	+
	31	+[[image:Illustration seg_flat_files.png]]
	32	+
	33	+== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
	34	+
	35	+
	36	+The Nutil software is currently compatible with:
	37	+
	38	+- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
	39	+
	40	+- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.

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