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 13.1
edited by puchades
on 2020/03/30 16:51
Change comment: Deleted image "Quantifier.PNG"

Summary

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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 -*
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 +* 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 +* //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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31 31  
32 32  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
33 33  
33 +
34 34  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35 35  
36 36  
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39 39  - Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 40  
41 41  - Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
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43 +
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