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1 -6. Quantification and spatial analysis with Nutil
1 +5. Quantification and spatial analysis with Nutil
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1 -== H2 Headings Will Appear in Table of Content ==
1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2 2  
3 +A detailed Nutil user manual is included when downloading the software.
3 3  
4 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
5 +[[image:Quantifier.PNG]]
5 5  
6 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
7 +**Basic steps:**
7 7  
8 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
9 +**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
9 9  
10 -=== H3 Headings Will Appear In The Table of Content ===
11 +It requires the following input:
11 11  
12 -==== You can also add images ====
13 +1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
13 13  
14 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
15 +**Requirement:**
15 15  
16 -Photo by David Clode
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 code in the //Excel template//.
17 17  
18 -==== Or code ====
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.
19 19  
20 -Code blocks can be added by using the code macro:
23 +(% start="2" %)
24 +1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
21 21  
22 -{{code language="python"}}
23 -x = 1
24 -if x == 1:
25 - # indented four spaces
26 - print("x is 1.")
27 -{{/code}}
26 +Generate the atlas maps in FLAT format with the //QuickNII //software
28 28  
29 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
28 +(% start="3" %)
29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 +1. (% style="color:#c0392b" %)**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). 
31 +
32 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
33 +
34 +
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Illustration seg_flat_files.png
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1 +XWiki.puchades
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Quantifier.PNG
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