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1 -== Nutil Quantifier ==
1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2 2  
3 -A detailed Nutil user manual is included when downloading the software.
3 +A detailed user manual is included when downloading the software.
4 4  
5 +[[image:Nutil_main.PNG]]
5 5  
6 6  **Basic steps:**
7 7  
8 -**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
9 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
9 9  
10 -(% start="1" style="list-style-type:decimal" %)
11 -1. **Segmentations with the labelling displayed in one RGB colour**
11 +It requires the following input:
12 12  
13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14 +
13 13  **Requirement:**
14 14  
15 -* must be 24-bit RGB images in PNG format
16 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
17 -* **//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//.
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).
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).
18 18  
19 19  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.
20 20  
21 21  (% start="2" %)
22 -1. **Customised anatomical atlas maps**
24 +1. (% style="color:#c0392b" %)**Customised atlas maps**
23 23  
24 -Generate the atlas maps in FLAT format with the //QuickNII //software
26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
25 25  
26 26  (% start="3" %)
27 -1. **Anchored XML** file generated with the //QuickNII// software.
28 -1. **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). 
29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
29 29  
30 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
31 +[[image:Illustration seg_flat_files.png]]
31 31  
33 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
32 32  
33 33  
34 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
35 -
36 +The Nutil software is currently compatible with:
37 +
38 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
39 +
40 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
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