Last modified by puchades on 2021/11/16 09:11
From version 2.4
edited by puchades
on 2020/03/25 15:30
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To version 3.2
edited by puchades
on 2020/03/25 17:01
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 5  **Basic steps:**
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7 7  **//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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9 9  (% start="1" style="list-style-type:decimal" %)
10 -1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
11 +1. **Segmentations with the labelling displayed in one RGB colour**
11 11  
12 12  **Requirement:**
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18 18  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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20 -1. **Customised anatomical atlas maps **(Right panel)
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22 +1. **Customised anatomical atlas maps**
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24 +Generate the atlas maps in FLAT format with the //QuickNII //software
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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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27 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). 
28 28  
30 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
29 29  
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 37  (% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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Illustration seg_flat_files.png
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