Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
From version 20.1
edited by puchades
on 2020/04/07 16:47
on 2020/04/07 16:47
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To version 26.1
edited by evanhancock
on 2020/07/21 09:39
on 2020/07/21 09:39
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... ... @@ -14,10 +14,9 @@ 14 14 15 15 **Requirement:** 16 16 17 -* 18 -** Input format: 24-bit RGB images in PNG 19 -** 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). 20 -** //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). 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). 21 21 22 22 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. 23 23 ... ... @@ -29,7 +29,7 @@ 29 29 (% start="3" %) 30 30 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. 31 31 32 -[[image:Illustration seg_flat_files.png ||height="254" width="500"]]31 +[[image:Illustration seg_flat_files.png]] 33 33 34 34 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 35 35 ... ... @@ -36,6 +36,5 @@ 36 36 37 37 The Nutil software is currently compatible with: 38 38 39 -- Allen mouse brain Atlas (CCFv3, 2015 or 2017) 40 - 41 -- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 38 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) 39 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.
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