Wiki source code of 5. Quantification and spatial analysis with Nutil
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2.2 | 1 | == Nutil Quantifier == |
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2.4 | 3 | A detailed Nutil user manual is included when downloading the software. |
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2.4 | 5 | **Basic steps:** |
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2.4 | 7 | **//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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2.4 | 9 | (% start="1" style="list-style-type:decimal" %) |
| 10 | 1. **Segmentations with the labelling displayed in one RGB colour **(Left panel) | ||
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2.4 | 12 | **Requirement:** |
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2.4 | 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//. | ||
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2.4 | 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. |
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2.4 | 20 | 1. **Customised anatomical atlas maps **(Right panel) |
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2.4 | 24 | Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]) |
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| 27 | 1. **Anchored XML** file generated with the //QuickNII// software. | ||
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| 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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1.1 | 37 | (% class="wikigeneratedid" id="HH4Won27tAppearinToC" %) |
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