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3	3	A detailed Nutil user manual is included when downloading the software.
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5		-[[image:Quantifier.PNG]]
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7	7	**Basic steps:**
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9	9	**//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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12		-1. **Segmentations with the labeling displayed in one RGB colour**
	10	+1. **Segmentations with the labelling displayed in one RGB colour**
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14	14	**Requirement:**
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16	16	* must be 24-bit RGB images in PNG format
17	17	* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
18		-* //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//.
	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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20	20	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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28	28	1. **Anchored XML** file generated with the //QuickNII// software.
29		-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).
	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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31		-[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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Quantifier.PNG

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1		-XWiki.puchades

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