Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -2,7 +2,7 @@ 2 2 3 3 A detailed user manual is included when downloading the software. 4 4 5 -[[image: Nutil_main.PNG]]5 +[[image:Quantifier.PNG]] 6 6 7 7 **Basic steps:** 8 8 ... ... @@ -10,12 +10,12 @@ 10 10 11 11 It requires the following input: 12 12 13 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour** 14 14 15 15 **Requirement:** 16 16 17 -* Inputformat:24-bit RGB images in PNG18 -* *The imageshave to have the sameaspectratio as the images used in QuickNII to generate the atlas maps (can be a different size).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 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). 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. ... ... @@ -30,6 +30,7 @@ 30 30 31 31 [[image:Illustration seg_flat_files.png||height="254" width="500"]] 32 32 33 + 33 33 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 34 34 35 35 ... ... @@ -38,3 +38,4 @@ 38 38 - Allen mouse brain Atlas (CCFv3, 2015 or 2017) 39 39 40 40 - Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 42 +