Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -2,33 +2,37 @@ 2 2 3 3 A detailed Nutil user manual is included when downloading the software. 4 4 5 -[[image:Quantifier.PNG]] 6 - 7 7 **Basic steps:** 8 8 9 9 **//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input: 10 10 11 11 (% start="1" style="list-style-type:decimal" %) 12 -1. **Segmentations with the labeling displayed in one RGB colour** 10 +1. **Segmentations with the labelling displayed in one RGB colour **(Left panel) 13 13 14 14 **Requirement:** 15 15 16 16 * must be 24-bit RGB images in PNG format 17 17 * same proportions as the images used in QuickNII to generate the atlas maps (can be a different size) 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//.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//. 19 19 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. 21 21 22 -(% start="2" %) 23 -1. **Customised anatomical atlas maps** 20 +1. **Customised anatomical atlas maps **(Right panel) 24 24 25 -Generate the atlas maps in FLAT format with the //QuickNII //software 26 26 27 -(% start="3" %) 23 + 24 +Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]]) 25 + 26 + 28 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). 30 30 31 -[[image:Illustration seg_flat_files.png||height="254" width="500"]] 32 32 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). 33 33 32 + 34 34 34 + 35 + 36 + 37 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %) 38 +
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