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  • Quantifier.PNG

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1		-== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
	1	+== Nutil Quantifier ==
2	2
3	3	A detailed Nutil user manual is included when downloading the software.
4	4
5		-[[image:Quantifier.PNG]]
6		-
7	7	**Basic steps:**
8	8
9		-**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
	7	+**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
10	10
11		-It requires the following input:
	9	+(% start="1" style="list-style-type:decimal" %)
	10	+1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
12	12
13		-1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
14		-
15	15	**Requirement:**
16	16
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//.
	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//.
20	20
21	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.
22	22
23		-(% start="2" %)
24		-1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
	20	+1. **Customised anatomical atlas maps **(Right panel)
25	25
26		-Generate the atlas maps in FLAT format with the //QuickNII //software.
27	27
28		-(% start="3" %)
29		-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).
31	31
32		-[[image:Illustration seg_flat_files.png||height="254" width="500"]]
	24	+Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]])
33	33
34	34
	27	+1. **Anchored XML** file generated with the //QuickNII// software.
	28	+
	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).
	31	+
	32	+
35	35
	34	+
	35	+
	36	+
	37	+(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
	38	+

Illustration seg_flat_files.png

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Quantifier.PNG

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