Last modified by puchades on 2021/11/16 09:11
From version 10.1
edited by sharoncy
on 2020/03/28 15:37
Change comment: There is no comment for this version
To version 30.1
edited by puchades
on 2020/09/24 13:04
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.sharoncy
1 +XWiki.puchades
Content
... ... @@ -2,8 +2,35 @@
2 2  
3 3  A detailed user manual is included when downloading the software.
4 4  
5 -[[image:Quantifier.PNG]]
5 +[[image:Nutil_GUI.png||style="float:left"]]
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 +
7 7  **Basic steps:**
8 8  
9 9  **//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
... ... @@ -10,12 +10,12 @@
10 10  
11 11  It requires the following input:
12 12  
13 -1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
40 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in a single RGB colour**
14 14  
15 15  **Requirement:**
16 16  
17 -* must be 24-bit RGB images in PNG format.
18 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size).
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).
19 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).
20 20  
21 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.
... ... @@ -28,12 +28,12 @@
28 28  (% start="3" %)
29 29  1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 30  
31 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
58 +[[image:Illustration seg_flat_files.png]]
32 32  
60 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
33 33  
34 -== (% style="color:#c0392b" %)Reference atlases available in //Nutil Quantifier//(%%) ==
35 35  
63 +The Nutil software is currently compatible with:
36 36  
37 -The Nutil software is currently compatible with the Allen mouse brain Atlas v3 (2015 or 2017) and the Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.
38 -
39 -
65 +* Allen mouse brain Atlas (CCFv3, 2015 or 2017)
66 +* Waxholm Space Atlas of the Sprague Dawley rat brain v2 or v3. 
Quantifier.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -37.8 KB
Content
Nutil_GUI.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +49.2 KB
Content
Nutil_main.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +51.2 KB
Content