Last modified by puchades on 2021/11/16 09:11
From version 2.3
edited by puchades
on 2020/03/25 15:16
Change comment: There is no comment for this version
To version 34.1
edited by puchades
on 2021/11/16 09:11
Change comment: There is no comment for this version

Summary

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1 -== Nutil Quantifier ==
1 +== (% style="color:#c0392b" %)//Nutil Quantifier//(%%) ==
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3 -A detailed Nutil user manual
3 +A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
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5 -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:Nutil_GUI.png||style="float:left"]]
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7 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
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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.
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11 -=== H3 Headings Will Appear In The Table of Content ===
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13 -==== You can also add images ====
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15 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
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17 -Photo by David Clode
18 18  
19 -==== Or code ====
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21 -Code blocks can be added by using the code macro:
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23 -{{code language="python"}}
24 -x = 1
25 -if x == 1:
26 - # indented four spaces
27 - print("x is 1.")
28 -{{/code}}
29 29  
30 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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36 +**Basic steps**
37 +
38 +//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
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40 +It requires the following input.
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42 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
43 +
44 +**Requirement**
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46 +* Input format: 24-bit RGB images in PNG.
47 +* 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).
48 +* //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 GUI (e.g., 255, 0, 0 for red).
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50 +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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52 +(% start="2" %)
53 +1. (% style="color:#c0392b" %)**Customised atlas maps**
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55 +Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
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57 +(% start="3" %)
58 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
59 +
60 +[[image:Illustration seg_flat_files.png]]
61 +
62 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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65 +The //Nutil //software is currently compatible with
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67 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
68 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4. 
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