Changes for page 5. Quantification and spatial analysis with Nutil
Last modified by puchades on 2021/11/16 09:11
Summary
-
Page properties (1 modified, 0 added, 0 removed)
-
Attachments (0 modified, 0 added, 2 removed)
Details
- Page properties
-
- Content
-
... ... @@ -2,35 +2,8 @@ 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 - 8 - 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 34 **Basic steps:** 35 35 36 36 **//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat). ... ... @@ -41,9 +41,10 @@ 41 41 42 42 **Requirement:** 43 43 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). 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). 47 47 48 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. 49 49 ... ... @@ -55,7 +55,7 @@ 55 55 (% start="3" %) 56 56 1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software. 57 57 58 -[[image:Illustration seg_flat_files.png]] 32 +[[image:Illustration seg_flat_files.png||height="254" width="500"]] 59 59 60 60 == (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) == 61 61 ... ... @@ -62,5 +62,6 @@ 62 62 63 63 The Nutil software is currently compatible with: 64 64 65 -* Allen mouse brain Atlas (CCFv3, 2015 or 2017) 66 -* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 39 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017) 40 + 41 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.
- Illustration seg_flat_files.png
-
- Author
-
... ... @@ -1,1 +1,0 @@ 1 -XWiki.puchades - Size
-
... ... @@ -1,1 +1,0 @@ 1 -79.2 KB - Content
- Nutil_GUI.png
-
- Author
-
... ... @@ -1,1 +1,0 @@ 1 -XWiki.puchades - Size
-
... ... @@ -1,1 +1,0 @@ 1 -49.2 KB - Content