Version 24.1 by puchades on 2020/04/07 16:51
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1 == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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3 A detailed user manual is included when downloading the software.
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5 [[image:Nutil_main.PNG]]
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7 **Basic steps:**
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9 **//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects 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 labelling displayed in a single RGB colour**
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15 **Requirement:**
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17 * Input format: 24-bit RGB images in PNG
18 * The images have to have the same aspect ratio 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 co//d//e in the GUI (e.g. 255, 0, 0 for red).
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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 atlas maps**
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26 Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
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29 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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31 [[image:Illustration seg_flat_files.png]]
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33 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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36 The Nutil software is currently compatible with:
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38 - Allen mouse brain Atlas (CCFv3, 2015 or 2017)
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40 - Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.