Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -1,30 +1,58 @@ 1 -== (% style="color:#c0392b" %)Nutil Quantifier(%%) == 1 +== (% style="color:#c0392b" %)//Nutil Quantifier//(%%) == 2 2 3 -A detailed user manual is includedwhendownloadingtheftware.3 +A detailed online user manual is found [[here>>https://nutil.readthedocs.io/en/latest/]]. 4 4 5 5 [[image:Nutil_GUI.png||style="float:left"]] 6 6 7 7 8 -**Basic steps:** 9 9 10 -**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). 11 11 12 -It requires the following input: 13 13 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 +**Basic steps** 37 + 38 +//Nutil Quantifier// quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent-brain section images (mouse or rat). 39 + 40 +It requires the following input. 41 + 14 14 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour** 15 15 16 -**Requirement :**44 +**Requirement** 17 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).46 +* Input format: 24-bit RGB images in PNG. 47 +* 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). 48 +* //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 GUI (e.g., 255, 0, 0 for red). 21 21 22 -To generate the segmentations we recommend the //Pixel and// //Object Classification workflows// in the //ilastik// software ( //ilastik.org//). However, any image50 +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 24 24 (% start="2" %) 25 25 1. (% style="color:#c0392b" %)**Customised atlas maps** 26 26 27 -Generate the atlas maps in FLAT format with the //QuickNII //software ( //or with VisuAlign//).55 +Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//). 28 28 29 29 (% start="3" %) 30 30 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. ... ... @@ -34,7 +34,7 @@ 34 34 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 35 35 36 36 37 -The Nutil software is currently compatible with :65 +The //Nutil //software is currently compatible with 38 38 39 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017) 40 -* Waxholm Space Atlas of the Sprague Dawley rat brain v2 orv3.67 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and 68 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4.