Last modified by puchades on 2021/11/16 09:11
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1 == (% style="color:#c0392b" %)//Nutil Quantifier//(%%) ==
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3 A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
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5 [[image:Nutil_GUI.png||style="float:left"]]
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36 **Basic steps**
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38 //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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40 It requires the following input.
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42 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
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44 **Requirement**
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46 * Input format: 24-bit RGB images in PNG.
47 * 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).
48 * //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 GUI (e.g., 255, 0, 0 for red).
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50 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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53 1. (% style="color:#c0392b" %)**Customised atlas maps**
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55 Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
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58 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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60 [[image:Illustration seg_flat_files.png]]
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62 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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65 The //Nutil //software is currently compatible with
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67 * Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
68 * Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4.