Wiki source code of 5. Quantification and spatial analysis with Nutil
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| author | version | line-number | content |
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| 1 | == Nutil Quantifier == | ||
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| 3 | A detailed Nutil user manual is included when downloading the software. | ||
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| 6 | **Basic steps:** | ||
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| 8 | **//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input: | ||
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| 10 | (% start="1" style="list-style-type:decimal" %) | ||
| 11 | 1. **Segmentations with the labelling displayed in one RGB colour** | ||
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| 13 | **Requirement:** | ||
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| 15 | * must be 24-bit RGB images in PNG format | ||
| 16 | * same proportions as the images used in QuickNII to generate the atlas maps (can be a different size) | ||
| 17 | * **//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//. | ||
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| 19 | 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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| 21 | (% start="2" %) | ||
| 22 | 1. **Customised anatomical atlas maps** | ||
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| 24 | Generate the atlas maps in FLAT format with the //QuickNII //software | ||
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| 26 | (% start="3" %) | ||
| 27 | 1. **Anchored XML** file generated with the //QuickNII// software. | ||
| 28 | 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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| 30 | [[image:Illustration seg_flat_files.png||height="254" width="500"]] | ||
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| 34 | (% class="wikigeneratedid" id="HH4Won27tAppearinToC" %) | ||
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