Summary

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  • Illustration seg_flat_files.png
  • Quantifier.PNG

Details

Page properties

Author

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1		-XWiki.sharoncy
	1	+XWiki.puchades

Content

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1		-== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
	1	+== H2 Headings Will Appear in Table of Content ==
2	2
3		-A detailed user manual is included when downloading the software.
4	4
5		-[[image:Quantifier.PNG]]
	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.
6	6
7		-**Basic steps:**
	6	+>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
8	8
9		-**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
	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.
10	10
11		-It requires the following input:
	10	+=== H3 Headings Will Appear In The Table of Content ===
12	12
13		-1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
	12	+==== You can also add images ====
14	14
15		-**Requirement:**
	14	+[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
16	16
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 co//d//e in the GUI (e.g. 255, 0, 0 for red).
	16	+Photo by David Clode
20	20
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.
	18	+==== Or code ====
22	22
23		-(% start="2" %)
24		-1. (% style="color:#c0392b" %)**Customised atlas maps**
	20	+Code blocks can be added by using the code macro:
25	25
26		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
	22	+{{code language="python"}}
	23	+x = 1
	24	+if x == 1:
	25	+ # indented four spaces
	26	+ print("x is 1.")
	27	+{{/code}}
27	27
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		-
34		-== (% style="color:#c0392b" %)Reference atlases available in //Nutil Quantifier//(%%) ==
35		-
36		-
37		-The Nutil software is currently compatible with the Allen mouse brain Atlas v3 (2015 or 2017) and the Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.
38		-
	29	+(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
39	39

Illustration seg_flat_files.png

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1		-XWiki.puchades

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Quantifier.PNG

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1		-XWiki.puchades

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