Version 7.1 by puchades on 2020/03/26 10:53
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1 == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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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 **Basic steps:**
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9 **//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
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11 It requires the following input:
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13 1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
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15 **Requirement:**
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17 * must be 24-bit RGB images in PNG format
18 * same proportions 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 code in the //Excel template//.
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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.
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24 1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
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26 Generate the atlas maps in FLAT format with the //QuickNII //software
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29 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 1. (% style="color:#c0392b" %)**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 [[image:Illustration seg_flat_files.png||height="254" width="500"]]
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