Last modified by puchades on 2021/11/16 09:11
From version 3.2
edited by puchades
on 2020/03/25 17:01
Change comment: There is no comment for this version
To version 5.2
edited by puchades
on 2020/03/25 17:05
Change comment: There is no comment for this version

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3 3  A detailed Nutil user manual is included when downloading the software.
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5 +[[image:Quantifier.PNG]]
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6 6  **Basic steps:**
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8 8  **//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
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10 10  (% start="1" style="list-style-type:decimal" %)
11 -1. **Segmentations with the labelling displayed in one RGB colour**
12 +1. **Segmentations with the labeling displayed in one RGB colour**
12 12  
13 13  **Requirement:**
14 14  
15 15  * must be 24-bit RGB images in PNG format
16 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//.
18 +* //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//.
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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.
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30 30  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
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Quantifier.PNG
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