Last modified by puchades on 2021/11/16 09:11
From version 2.4
edited by puchades
on 2020/03/25 15:30
Change comment: There is no comment for this version
To version 10.1
edited by sharoncy
on 2020/03/28 15:37
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.puchades
1 +XWiki.sharoncy
Content
... ... @@ -1,38 +1,39 @@
1 -== Nutil Quantifier ==
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 +[[image:Quantifier.PNG]]
6 +
5 5  **Basic steps:**
6 6  
7 -**//Quantifier//** locates and quantifies labelling 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).
8 8  
9 -(% start="1" style="list-style-type:decimal" %)
10 -1. **Segmentations with the labelling displayed in one RGB colour **(Left panel)
11 +It requires the following input:
11 11  
13 +1. (% style="color:#c0392b" %)**Segmentations with the labelling displayed in one RGB colour**
14 +
12 12  **Requirement:**
13 13  
14 -* must be 24-bit RGB images in PNG format
15 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
16 -* **//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).
17 17  
18 18  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.
19 19  
20 -1. **Customised anatomical atlas maps **(Right panel)
23 +(% start="2" %)
24 +1. (% style="color:#c0392b" %)**Customised atlas maps**
21 21  
26 +Generate the atlas maps in FLAT format with the //QuickNII //software (//or with VisuAlign//).
22 22  
28 +(% start="3" %)
29 +1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
23 23  
24 -Generate the atlas maps in FLAT format with the //QuickNII //software ([[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]])
31 +[[image:Illustration seg_flat_files.png||height="254" width="500"]]
25 25  
26 26  
27 -1. **Anchored XML** file generated with the //QuickNII// software.
34 +== (% style="color:#c0392b" %)Reference atlases available in //Nutil Quantifier//(%%) ==
28 28  
29 29  
30 -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).
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.
31 31  
32 -
33 33  
34 -
35 -
36 -
37 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
38 -
Illustration seg_flat_files.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +79.2 KB
Content
Quantifier.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +37.8 KB
Content