Last modified by puchades on 2021/11/16 09:11

From version 13.1
edited by puchades
on 2020/03/30 16:51
Change comment: Deleted image "Quantifier.PNG"
To version 8.1
edited by puchades
on 2020/03/26 10:53
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1 1  == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2 2  
3 -A detailed user manual is included when downloading the software.
3 +A detailed Nutil user manual is included when downloading the software.
4 4  
5 5  [[image:Quantifier.PNG]]
6 6  
7 7  **Basic steps:**
8 8  
9 -**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
9 +**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
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**
13 +1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
14 14  
15 15  **Requirement:**
16 16  
17 17  * must be 24-bit RGB images in PNG format.
18 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).
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 code in the //Excel template//.
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.
22 22  
23 23  (% start="2" %)
24 -1. (% style="color:#c0392b" %)**Customised atlas maps**
24 +1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
25 25  
26 -Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
26 +Generate the atlas maps in FLAT format with the //QuickNII //software.
27 27  
28 28  (% start="3" %)
29 29  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 +1. (% style="color:#c0392b" %)**Reference atlas label file**(%%) (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the //Nutil// package (in the “Labels” folder). 
30 30  
31 31  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 32  
33 33  
34 -== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35 -
36 -
37 -The Nutil software is currently compatible with:
38 -
39 -- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 -
41 -- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
42 -
43 43  
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