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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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5	5	**Basic steps:**
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7	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	9	(% start="1" style="list-style-type:decimal" %)
10		-1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
	12	+1. **Segmentations with the labeling displayed in one RGB colour**
11	11
12	12	**Requirement:**
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14	14	* must be 24-bit RGB images in PNG format
15	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//.
	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//.
17	17
18	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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20		-1. **Customised anatomical atlas maps **(Right panel)
	22	+(% start="2" %)
	23	+1. **Customised anatomical atlas maps**
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	25	+Generate the atlas maps in FLAT format with the //QuickNII //software
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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]])
25		-
26		-
	27	+(% start="3" %)
27	27	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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32		-
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34		-
35		-
36		-
37		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
38		-

Illustration seg_flat_files.png

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Quantifier.PNG

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