Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
From version 32.1
edited by annedevismes
on 2021/06/08 11:56
on 2021/06/08 11:56
Change comment:
There is no comment for this version
Summary
-
Page properties (2 modified, 0 added, 0 removed)
Details
- Page properties
-
- Author
-
... ... @@ -1,1 +1,1 @@ 1 -XWiki.a nnedevismes1 +XWiki.puchades - Content
-
... ... @@ -1,58 +1,29 @@ 1 -== (% style="color:#c0392b" %) //Nutil Quantifier//(%%) ==1 +== (% style="color:#c0392b" %)Nutil Quantifier(%%) == 2 2 3 3 A detailed user manual is included when downloading the software. 4 4 5 -[[image:Nutil_ GUI.png||style="float:left"]]5 +[[image:Nutil_main.PNG]] 6 6 7 +**Basic steps:** 7 7 9 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). 8 8 11 +It requires the following input: 9 9 10 - 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 - 42 42 1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour** 43 43 44 -**Requirement** 15 +**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).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). 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.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. 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//).26 +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 with36 +The Nutil software is currently compatible with: 66 66 67 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017) and38 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017) 68 68 * Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3.