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7	7	**Basic steps:**
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9		-**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
	9	+**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat).
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11		-(% start="1" style="list-style-type:decimal" %)
12		-1. **Segmentations with the labeling displayed in one RGB colour**
	11	+It requires the following input:
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	13	+1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
	14	+
14	14	**Requirement:**
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16	16	* must be 24-bit RGB images in PNG format
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20	20	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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22	22	(% start="2" %)
23		-1. **Customised anatomical atlas maps**
	24	+1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
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25	25	Generate the atlas maps in FLAT format with the //QuickNII //software
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27	27	(% start="3" %)
28		-1. **Anchored XML** file generated with the //QuickNII// software.
29		-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).
	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).
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31	31	[[image:Illustration seg_flat_files.png||height="254" width="500"]]
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