Last modified by puchades on 2021/11/16 09:11

From version 6.1
edited by puchades
on 2020/03/26 10:49
Change comment: There is no comment for this version
To version 14.1
edited by puchades
on 2020/03/30 16:51
Change comment: Deleted image "Illustration seg_flat_files.png"

Summary

Details

Page properties
Content
... ... @@ -1,34 +1,43 @@
1 1  == (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
2 2  
3 -A detailed Nutil user manual is included when downloading the software.
3 +A detailed user manual is included when downloading the software.
4 4  
5 5  [[image:Quantifier.PNG]]
6 6  
7 7  **Basic steps:**
8 8  
9 -**//Quantifier//** locates and quantifies labeling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
9 +**//Nutil Quantifier//** quantifies and assigns anatomical location to labelled objects identified by segmentation in rodent brain section images (mouse or rat).
10 10  
11 -(% start="1" style="list-style-type:decimal" %)
12 -1. **Segmentations with the labeling displayed in one RGB colour**
11 +It requires the following input:
13 13  
13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
14 +
14 14  **Requirement:**
15 15  
16 -* must be 24-bit RGB images in PNG format
17 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
18 -* //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 //Excel template//.
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).
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).
19 19  
20 20  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 21  
22 22  (% start="2" %)
23 -1. **Customised anatomical atlas maps**
24 +1. (% style="color:#c0392b" %)**Customised atlas maps**
24 24  
25 -Generate the atlas maps in FLAT format with the //QuickNII //software
26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
26 26  
27 27  (% start="3" %)
28 -1. **Anchored XML** file generated with the //QuickNII// software.
29 -1. **Reference atlas label file** (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the //Nutil// package (in the “Labels” folder). 
29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 30  
31 31  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 32  
33 33  
34 +== (% style="color:#c0392b" %)Reference atlases in //Nutil Quantifier//(%%) ==
35 +
36 +
37 +The Nutil software is currently compatible with:
38 +
39 +- Allen mouse brain Atlas (CCFv3, 2015 or 2017)
40 +
41 +- Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3. 
42 +
34 34  
Illustration seg_flat_files.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -79.2 KB
Content
Quantifier.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -37.8 KB
Content