Last modified by puchades on 2021/11/16 09:11
From version 27.1
edited by puchades
on 2020/09/24 13:01
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To version 33.1
edited by puchades
on 2021/11/16 09:10
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1 -== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
1 +== (% style="color:#c0392b" %)//Nutil Quantifier//(%%) ==
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3 -A detailed user manual is included when downloading the software.
3 +A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
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5 -[[image:Nutil_main.PNG]]
5 +[[image:Nutil_GUI.png||style="float:left"]]
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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13 13  1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14 14  
15 -**Requirement:**
44 +**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).
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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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.
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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23 23  (% start="2" %)
24 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//).
55 +Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
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29 29  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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33 33  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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36 -The Nutil software is currently compatible with:
65 +The //Nutil //software is currently compatible with
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38 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
67 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
39 39  * Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
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