Last modified by puchades on 2021/11/16 09:11
From version 30.1
edited by puchades
on 2020/09/24 13:04
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To version 20.1
edited by puchades
on 2020/04/07 16:47
Change comment: There is no comment for this version

Summary

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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]]
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34 34  **Basic steps:**
35 35  
36 36  **//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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41 41  
42 42  **Requirement:**
43 43  
44 -* Input format: 24-bit RGB images in PNG
45 -* 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).
46 -* //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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18 +** Input format: 24-bit RGB images in PNG
19 +** 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).
20 +** //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).
47 47  
48 48  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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55 55  (% start="3" %)
56 56  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
57 57  
58 -[[image:Illustration seg_flat_files.png]]
32 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
59 59  
60 60  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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63 63  The Nutil software is currently compatible with:
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65 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
66 -* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
39 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
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41 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
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