Version 5.1 by puchades on 2020/03/25 17:04
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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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5 [[image:Quantifier.PNG]]
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7 **Basic steps:**
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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**
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14 **Requirement:**
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16 * must be 24-bit RGB images in PNG format
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//.
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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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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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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"]]