Last modified by puchades on 2021/11/16 09:11
From version 20.1
edited by puchades
on 2020/04/07 16:47
Change comment: There is no comment for this version
To version 26.1
edited by evanhancock
on 2020/07/21 09:39
Change comment: There is no comment for this version

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14 14  
15 15  **Requirement:**
16 16  
17 -*
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).
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).
21 21  
22 22  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.
23 23  
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29 29  (% start="3" %)
30 30  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
31 31  
32 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
31 +[[image:Illustration seg_flat_files.png]]
33 33  
34 34  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35 35  
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36 36  
37 37  The Nutil software is currently compatible with:
38 38  
39 -- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 -
41 -- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
38 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
39 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
Illustration seg_flat_files.png
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