Summary

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Details

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1	1	== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
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3		-A detailed user manual is included when downloading the software.
	3	+A detailed Nutil user manual is included when downloading the software.
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5		-[[image:Nutil_GUI.png||style="float:left"]]
	5	+[[image:Quantifier.PNG]]
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34	34	**Basic steps:**
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36		-**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
	9	+**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
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38		-It requires the following input:
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	12	+1. **Segmentations with the labeling displayed in one RGB colour**
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40		-1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
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42	42	**Requirement:**
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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).
	16	+* must be 24-bit RGB images in PNG format
	17	+* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
	18	+* //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//.
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48	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.
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51		-1. (% style="color:#c0392b" %)**Customised atlas maps**
	23	+1. **Customised anatomical atlas maps**
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53		-Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
	25	+Generate the atlas maps in FLAT format with the //QuickNII //software
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56		-1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	28	+1. **Anchored XML** file generated with the //QuickNII// software.
	29	+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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58		-[[image:Illustration seg_flat_files.png]]
	31	+[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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60		-== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
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63		-The Nutil software is currently compatible with:
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65		-* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
66		-* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.
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