Last modified by puchades on 2021/11/16 09:11
From version 10.1
edited by sharoncy
on 2020/03/28 15:37
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To version 2.4
edited by puchades
on 2020/03/25 15:30
Change comment: There is no comment for this version

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1 -== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
1 +== 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 -[[image:Quantifier.PNG]]
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).
7 +**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
10 10  
11 -It requires the following input:
9 +(% start="1" style="list-style-type:decimal" %)
10 +1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
12 12  
13 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
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).
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).
14 +* must be 24-bit RGB images in PNG format
15 +* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
16 +* **//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 -(% start="2" %)
24 -1. (% style="color:#c0392b" %)**Customised atlas maps**
20 +1. **Customised anatomical atlas maps **(Right panel)
25 25  
26 -Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
27 27  
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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"]]
24 +Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]])
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33 33  
34 -== (% style="color:#c0392b" %)Reference atlases available in //Nutil Quantifier//(%%) ==
27 +1. **Anchored XML** file generated with the //QuickNII// software.
35 35  
36 36  
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.
30 +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).
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37 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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Illustration seg_flat_files.png
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