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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10.1 | 3 | A detailed user manual is included when downloading the software. |
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17.1 | 5 | [[image:Nutil_main.PNG]] |
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3.2 | 6 | |
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2.4 | 7 | **Basic steps:** |
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10.1 | 9 | **//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). |
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1.1 | 10 | |
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7.1 | 11 | It requires the following input: |
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1.1 | 12 | |
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19.2 | 13 | 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour** |
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7.1 | 14 | |
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2.4 | 15 | **Requirement:** |
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1.1 | 16 | |
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21.1 | 17 | * Input format: 24-bit RGB images in PNG |
| 18 | * The images have to have the same aspect ratio 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 co//d//e in the GUI (e.g. 255, 0, 0 for red). | ||
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1.1 | 20 | |
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2.4 | 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. |
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1.1 | 22 | |
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2.5 | 23 | (% start="2" %) |
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10.1 | 24 | 1. (% style="color:#c0392b" %)**Customised atlas maps** |
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1.1 | 25 | |
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10.1 | 26 | Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//). |
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1.1 | 27 | |
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2.5 | 28 | (% start="3" %) |
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7.1 | 29 | 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. |
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2.4 | 30 | |
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23.1 | 31 | [[image:Illustration seg_flat_files.png]] |
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2.4 | 32 | |
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11.1 | 33 | == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == |
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10.1 | 34 | |
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12.1 | 36 | The Nutil software is currently compatible with: |
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10.1 | 37 | |
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12.1 | 38 | - Allen mouse brain Atlas (CCFv3, 2015 or 2017) |
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23.2 | 40 | - Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. |