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1		-== Nutil Quantifier ==
	1	+== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2	2
3		-A detailed Nutil user manual is included when downloading the software.
	3	+A detailed user manual is included when downloading the software.
4	4
5		-**Basic steps:**
	5	+[[image:Nutil_GUI.png||style="float:left"]]
6	6
7		-**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
8	8
9		-(% start="1" style="list-style-type:decimal" %)
10		-1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
11	11
12		-**Requirement:**
13	13
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//.
17	17
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.
19	19
20		-1. **Customised anatomical atlas maps **(Right panel)
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22	22
23	23
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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26	26
27		-1. **Anchored XML** file generated with the //QuickNII// software.
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29	29
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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32	32
33		-
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35		-
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37		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
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	24	+
	25	+
	26	+
	27	+
	28	+
	29	+
	30	+
	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//).
	54	+
	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.

Illustration seg_flat_files.png

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