Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
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... ... @@ -1,6 +1,6 @@ 1 -== (% style="color:#c0392b" %) //Nutil Quantifier//(%%) ==1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) == 2 2 3 -A detailed onlineuser manual isfound[[here>>https://nutil.readthedocs.io/en/latest/]].3 +A detailed user manual is included when downloading the software. 4 4 5 5 [[image:Nutil_GUI.png||style="float:left"]] 6 6 ... ... @@ -31,28 +31,26 @@ 31 31 32 32 33 33 34 +**Basic steps:** 34 34 36 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). 35 35 36 - **Basicsteps**38 +It requires the following input: 37 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 - 42 42 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour** 43 43 44 -**Requirement** 42 +**Requirement:** 45 45 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).44 +* Input format: 24-bit RGB images in PNG 45 +* 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). 46 +* //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). 49 49 50 -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.48 +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. 51 51 52 52 (% start="2" %) 53 53 1. (% style="color:#c0392b" %)**Customised atlas maps** 54 54 55 -Generate the atlas maps in FLAT format with the //QuickNII //software (or with //VisuAlign//).53 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//). 56 56 57 57 (% start="3" %) 58 58 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. ... ... @@ -62,7 +62,7 @@ 62 62 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 63 63 64 64 65 -The //Nutil//software is currently compatible with63 +The Nutil software is currently compatible with: 66 66 67 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and65 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) 68 68 * Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.