Wiki source code of 5. Quantification and spatial analysis with Nutil
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6.1 | 1 | == (% style="color:#c0392b" %)Nutil Quantifier(%%) == |
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1.1 | 2 | |
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2.4 | 3 | A detailed Nutil user manual is included when downloading the software. |
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1.1 | 4 | |
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5.1 | 5 | [[image:Quantifier.PNG]] |
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3.2 | 6 | |
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2.4 | 7 | **Basic steps:** |
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1.1 | 8 | |
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5.4 | 9 | **//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input: |
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1.1 | 10 | |
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2.4 | 11 | (% start="1" style="list-style-type:decimal" %) |
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5.1 | 12 | 1. **Segmentations with the labeling displayed in one RGB colour** |
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1.1 | 13 | |
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2.4 | 14 | **Requirement:** |
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1.1 | 15 | |
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2.4 | 16 | * must be 24-bit RGB images in PNG format |
| 17 | * same proportions as the images used in QuickNII to generate the atlas maps (can be a different size) | ||
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5.2 | 18 | * //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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1.1 | 19 | |
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2.4 | 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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1.1 | 21 | |
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2.5 | 22 | (% start="2" %) |
| 23 | 1. **Customised anatomical atlas maps** | ||
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1.1 | 24 | |
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2.5 | 25 | Generate the atlas maps in FLAT format with the //QuickNII //software |
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1.1 | 26 | |
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2.5 | 27 | (% start="3" %) |
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2.4 | 28 | 1. **Anchored XML** file generated with the //QuickNII// software. |
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3.2 | 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). |
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2.4 | 30 | |
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3.2 | 31 | [[image:Illustration seg_flat_files.png||height="254" width="500"]] |
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2.4 | 32 | |
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5.2 | 34 |