Last modified by puchades on 2021/11/16 09:11
From version 4.1
edited by puchades
on 2020/03/25 17:03
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To version 2.4
edited by puchades
on 2020/03/25 15:30
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Summary

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3 3  A detailed Nutil user manual is included when downloading the software.
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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**
10 +1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
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13 13  **Requirement:**
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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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22 -1. **Customised anatomical atlas maps**
20 +1. **Customised anatomical atlas maps **(Right panel)
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24 -Generate the atlas maps in FLAT format with the //QuickNII //software
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26 -(% start="3" %)
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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). 
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30 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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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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34 34  (% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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Illustration seg_flat_files.png
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Quantifier.PNG
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