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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	7	+**Basic steps:**
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	9	+**//Nutil Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
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	11	+It requires the following input:
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	13	+1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
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	15	+**Requirement:**
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	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 code in the //Excel template//.
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	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.
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36		-**Basic steps**
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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**
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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	52	(% start="2" %)
53		-1. (% style="color:#c0392b" %)**Customised atlas maps**
	24	+1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
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55		-Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
	26	+Generate the atlas maps in FLAT format with the //QuickNII //software.
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58	58	1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	30	+1. (% style="color:#c0392b" %)**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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60		-[[image:Illustration seg_flat_files.png]]
	32	+[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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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 or v3.
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