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  • Quantifier.PNG

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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		-**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
	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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11	11	(% start="1" style="list-style-type:decimal" %)
12		-1. **Segmentations with the labeling displayed in one RGB colour**
	10	+1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
13	13
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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22		-(% start="2" %)
23		-1. **Customised anatomical atlas maps**
	20	+1. **Customised anatomical atlas maps **(Right panel)
24	24
25		-Generate the atlas maps in FLAT format with the //QuickNII //software
26	26
27		-(% start="3" %)
	23	+
	24	+Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]])
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	26	+
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).
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31		-[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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	30	+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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	35	+
	36	+
	37	+(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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Illustration seg_flat_files.png

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Quantifier.PNG

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