Last modified by puchades on 2021/11/16 09:11
From version 19.1
edited by puchades
on 2020/03/30 17:16
Change comment: There is no comment for this version
To version 29.1
edited by puchades
on 2020/09/24 13:04
Change comment: There is no comment for this version

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:Nutil_GUI.png||style="float:left"]]
6 6  
7 +
7 7  **Basic steps:**
8 8  
9 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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10 10  
11 11  It requires the following input:
12 12  
13 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
14 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14 14  
15 15  **Requirement:**
16 16  
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).
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).
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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28 28  (% start="3" %)
29 29  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 30  
31 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 +[[image:Illustration seg_flat_files.png]]
32 32  
33 33  == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
34 34  
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35 35  
36 36  The Nutil software is currently compatible with:
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 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
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