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1	1	== Nutil Quantifier ==
2	2
3		-A detailed Nutil user manual
	3	+A detailed Nutil user manual is included when downloading the software.
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	5	+**Basic steps:**
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	+**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
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	9	+(% start="1" style="list-style-type:decimal" %)
	10	+1. **Segmentations with the labelling displayed in one RGB colour**
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11		-=== H3 Headings Will Appear In The Table of Content ===
	12	+**Requirement:**
12	12
13		-==== You can also add images ====
	14	+* must be 24-bit RGB images in PNG format
	15	+* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
	16	+* **//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//.
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15		-[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
	18	+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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17		-Photo by David Clode
	20	+(% start="2" %)
	21	+1. **Customised anatomical atlas maps**
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19		-==== Or code ====
	23	+Generate the atlas maps in FLAT format with the //QuickNII //software
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21		-Code blocks can be added by using the code macro:
	25	+(% start="3" %)
	26	+1. **Anchored XML** file generated with the //QuickNII// software.
	27	+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).
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23		-{{code language="python"}}
24		-x = 1
25		-if x == 1:
26		- # indented four spaces
27		- print("x is 1.")
28		-{{/code}}
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30	30	(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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