Last modified by puchades on 2021/11/16 09:11
From version 29.1
edited by puchades
on 2020/09/24 13:04
Change comment: There is no comment for this version
To version 10.1
edited by sharoncy
on 2020/03/28 15:37
Change comment: There is no comment for this version

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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_GUI.png||style="float:left"]]
5 +[[image:Quantifier.PNG]]
6 6  
7 -
8 8  **Basic steps:**
9 9  
10 10  **//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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11 11  
12 12  It requires the following input:
13 13  
14 -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**
15 15  
16 16  **Requirement:**
17 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).
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).
20 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).
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.
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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]]
31 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
33 33  
34 -== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35 35  
34 +== (% style="color:#c0392b" %)Reference atlases available in //Nutil Quantifier//(%%) ==
36 36  
37 -The Nutil software is currently compatible with:
38 38  
39 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 -* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
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.
38 +
39 +
Nutil_GUI.png
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