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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	+[[image:Nutil_main.PNG]]
	6	+
5	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:
	9	+**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
8	8
9		-(% start="1" style="list-style-type:decimal" %)
10		-1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
	11	+It requires the following input:
11	11
	13	+1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
	14	+
12	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	+* Input format: 24-bit RGB images in PNG
	18	+* 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).
	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).
17	17
18	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)
	23	+(% start="2" %)
	24	+1. (% style="color:#c0392b" %)**Customised atlas maps**
21	21
	26	+Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
22	22
	28	+(% start="3" %)
	29	+1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
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]])
	31	+[[image:Illustration seg_flat_files.png||height="254" width="500"]]
25	25
	33	+== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
26	26
27		-1. **Anchored XML** file generated with the //QuickNII// software.
28	28
	36	+The Nutil software is currently compatible with:
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).
	38	+- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
31	31
32		-
33		-
34		-
35		-
36		-
37		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
38		-
	40	+- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.

Nutil_main.PNG

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