Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -1,34 +1,43 @@ 1 1 == (% style="color:#c0392b" %)Nutil Quantifier(%%) == 2 2 3 -A detailed Nutil user manual is included when downloading the software.3 +A detailed user manual is included when downloading the software. 4 4 5 5 [[image:Quantifier.PNG]] 6 6 7 7 **Basic steps:** 8 8 9 -**//Quantifier//** locates andquantifieslabelingidentified by segmentation in rodent brain section images (mouse or rat).It requires the following input:9 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). 10 10 11 -(% start="1" style="list-style-type:decimal" %) 12 -1. **Segmentations with the labeling displayed in one RGB colour** 11 +It requires the following input: 13 13 13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour** 14 + 14 14 **Requirement:** 15 15 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) 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 //Exceltemplate//.17 +* must be 24-bit RGB images in PNG format. 18 +* same proportions 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). 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 22 (% start="2" %) 23 -1. **Customised a natomicaltlas maps**24 +1. (% style="color:#c0392b" %)**Customised atlas maps** 24 24 25 -Generate the atlas maps in FLAT format with the //QuickNII //software 26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//). 26 26 27 27 (% start="3" %) 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). 29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. 30 30 31 31 [[image:Illustration seg_flat_files.png||height="254" width="500"]] 32 32 33 33 34 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 35 + 36 + 37 +The Nutil software is currently compatible with: 38 + 39 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017) 40 + 41 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 42 + 34 34
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