Summary

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1		-== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
	1	+== Nutil Quantifier ==
2	2
3		-A detailed user manual is included when downloading the software.
	3	+A detailed Nutil user manual is included when downloading the software.
4	4
5		-[[image:Nutil_GUI.png||style="float:left"]]
	5	+**Basic steps:**
6	6
	7	+**//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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	9	+(% start="1" style="list-style-type:decimal" %)
	10	+1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
8	8
	12	+**Requirement:**
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	14	+* must be 24-bit RGB images in PNG format
	15	+* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
	16	+* **//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//.
10	10
	18	+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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	20	+1. **Customised anatomical atlas maps **(Right panel)
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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	+1. **Anchored XML** file generated with the //QuickNII// software.
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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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	35	+
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23		-
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31		-
32		-
33		-
34		-**Basic steps:**
35		-
36		-**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
37		-
38		-It requires the following input:
39		-
40		-1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
41		-
42		-**Requirement:**
43		-
44		-* Input format: 24-bit RGB images in PNG
45		-* 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).
46		-* //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).
47		-
48		-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.
49		-
50		-(% start="2" %)
51		-1. (% style="color:#c0392b" %)**Customised atlas maps**
52		-
53		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
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55		-(% start="3" %)
56		-1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
57		-
58		-[[image:Illustration seg_flat_files.png]]
59		-
60		-== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
61		-
62		-
63		-The Nutil software is currently compatible with:
64		-
65		-* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
66		-* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.
	37	+(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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Illustration seg_flat_files.png

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