Last modified by puchades on 2021/11/16 09:11
From version 31.2
edited by annedevismes
on 2021/06/08 11:01
Change comment: There is no comment for this version
To version 28.1
edited by puchades
on 2020/09/24 13:03
Change comment: Uploaded new attachment "Nutil_GUI.png", version {1}

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1 -XWiki.annedevismes
1 +XWiki.puchades
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3 3  A detailed user manual is included when downloading the software.
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5 -[[image:Nutil_GUI.png||style="float:left"]]
5 +[[image:Nutil_main.PNG]]
6 6  
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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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 42  1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
43 43  
44 -**Requirement**
15 +**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).
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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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.
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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52 52  (% start="2" %)
53 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//).
26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
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57 57  (% start="3" %)
58 58  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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62 62  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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65 -The //Nutil //software is currently compatible with
36 +The Nutil software is currently compatible with:
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67 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
38 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
68 68  * Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.