Last modified by puchades on 2021/11/16 09:11
From version 2.3
edited by puchades
on 2020/03/25 15:16
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To version 22.1
edited by puchades
on 2020/04/07 16:50
Change comment: Uploaded new attachment "Illustration seg_flat_files.png", version {1}

Summary

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1 -== Nutil Quantifier ==
1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2 2  
3 -A detailed Nutil user manual
3 +A detailed user manual is included when downloading the software.
4 4  
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5 +[[image:Nutil_main.PNG]]
6 6  
7 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
7 +**Basic steps:**
8 8  
9 -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 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
10 10  
11 -=== H3 Headings Will Appear In The Table of Content ===
11 +It requires the following input:
12 12  
13 -==== You can also add images ====
13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14 14  
15 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
15 +**Requirement:**
16 16  
17 -Photo by David Clode
17 +* Input format: 24-bit RGB images in PNG
18 +* The images have to have the same aspect ratio 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).
18 18  
19 -==== 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.
20 20  
21 -Code blocks can be added by using the code macro:
23 +(% start="2" %)
24 +1. (% style="color:#c0392b" %)**Customised atlas maps**
22 22  
23 -{{code language="python"}}
24 -x = 1
25 -if x == 1:
26 - # indented four spaces
27 - print("x is 1.")
28 -{{/code}}
26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
29 29  
30 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
31 -
28 +(% start="3" %)
29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 +
31 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 +
33 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
34 +
35 +
36 +The Nutil software is currently compatible with:
37 +
38 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
39 +
40 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
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