Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -1,43 +1,35 @@ 1 1 == (% style="color:#c0392b" %)Nutil Quantifier(%%) == 2 2 3 -A detailed user manual is included when downloading the software. 3 +A detailed Nutil user manual is included when downloading the software. 4 4 5 5 [[image:Quantifier.PNG]] 6 6 7 7 **Basic steps:** 8 8 9 -**//Nutil Quantifier//** quantifies and assigns anatomical locationtolabelledobjectsidentified by segmentation in rodent brain section images (mouse or rat).9 +**//Nutil Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). 10 10 11 11 It requires the following input: 12 12 13 -1. (% style="color:#c0392b" %)**Segmentations with the label ling displayed in one RGB colour**13 +1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour** 14 14 15 15 **Requirement:** 16 16 17 17 * must be 24-bit RGB images in PNG format. 18 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 theGUI (e.g.255, 0, 0 for red).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 code in the //Excel template//. 20 20 21 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. 22 22 23 23 (% start="2" %) 24 -1. (% style="color:#c0392b" %)**Customised atlas maps** 24 +1. (% style="color:#c0392b" %)**Customised anatomical atlas maps** 25 25 26 -Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).26 +Generate the atlas maps in FLAT format with the //QuickNII //software. 27 27 28 28 (% start="3" %) 29 29 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. 30 +1. (% style="color:#c0392b" %)**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 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 - 43 43
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