Version 4.1 by puchades on 2020/03/25 17:03
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1 == Nutil Quantifier ==
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3 A detailed Nutil user manual is included when downloading the software.
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6 **Basic steps:**
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8 **//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 1. **Segmentations with the labelling displayed in one RGB colour**
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13 **Requirement:**
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15 * must be 24-bit RGB images in PNG format
16 * same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
17 * **//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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19 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 1. **Customised anatomical atlas maps**
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24 Generate the atlas maps in FLAT format with the //QuickNII //software
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27 1. **Anchored XML** file generated with the //QuickNII// software.
28 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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30 [[image:Illustration seg_flat_files.png||height="254" width="500"]]
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