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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 online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]].
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)
21	21
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]])
25	25
26	26
27		-1. **Anchored XML** file generated with the //QuickNII// software.
28	28
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		-
34	34
35		-
36	36
37		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
38		-
	23	+
	24	+
	25	+
	26	+
	27	+
	28	+
	29	+
	30	+
	31	+
	32	+
	33	+
	34	+
	35	+
	36	+**Basic steps**
	37	+
	38	+//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat).
	39	+
	40	+It requires the following input.
	41	+
	42	+1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
	43	+
	44	+**Requirement**
	45	+
	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).
	49	+
	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.
	51	+
	52	+(% start="2" %)
	53	+1. (% style="color:#c0392b" %)**Customised atlas maps**
	54	+
	55	+Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).
	56	+
	57	+(% start="3" %)
	58	+1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
	59	+
	60	+[[image:Illustration seg_flat_files.png]]
	61	+
	62	+== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
	63	+
	64	+
	65	+The //Nutil //software is currently compatible with
	66	+
	67	+* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
	68	+* Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4.

Illustration seg_flat_files.png

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