Last modified by puchades on 2021/11/16 09:11
From version 19.2
edited by puchades
on 2020/04/07 16:46
Change comment: There is no comment for this version
To version 11.1
edited by sharoncy
on 2020/03/28 15:37
Change comment: There is no comment for this version

Summary

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1 -XWiki.puchades
1 +XWiki.sharoncy
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2 2  
3 3  A detailed user manual is included when downloading the software.
4 4  
5 -[[image:Nutil_main.PNG]]
5 +[[image:Quantifier.PNG]]
6 6  
7 7  **Basic steps:**
8 8  
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10 10  
11 11  It requires the following input:
12 12  
13 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
14 14  
15 15  **Requirement:**
16 16  
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).
17 +* must be 24-bit RGB images in PNG format.
18 +* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size).
19 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).
20 20  
21 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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30 30  
31 31  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 32  
33 +
33 33  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
34 34  
35 35  
36 -The Nutil software is currently compatible with:
37 +The Nutil software is currently compatible with the Allen mouse brain Atlas v3 (2015 or 2017) and the Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
37 37  
38 -- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
39 -
40 -- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
39 +
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