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

From version 8.1
edited by puchades
on 2020/03/26 10:53
Change comment: There is no comment for this version
To version 5.3
edited by puchades
on 2020/03/25 17:05
Change comment: There is no comment for this version

Summary

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1 -== (% style="color:#c0392b" %)Nutil Quantifier(%%) ==
1 +== Nutil Quantifier ==
2 2  
3 3  A detailed Nutil user manual is included when downloading the software.
4 4  
... ... @@ -6,28 +6,27 @@
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).
9 +**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
10 10  
11 -It requires the following input:
11 +(% start="1" style="list-style-type:decimal" %)
12 +1. **Segmentations with the labeling displayed in one RGB colour**
12 12  
13 -1. (% style="color:#c0392b" %)**Segmentations with the labeling displayed in one RGB colour**
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).
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)
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 code in the //Excel template//.
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.
22 22  
23 23  (% start="2" %)
24 -1. (% style="color:#c0392b" %)**Customised anatomical atlas maps**
23 +1. **Customised anatomical atlas maps**
25 25  
26 -Generate the atlas maps in FLAT format with the //QuickNII //software.
25 +Generate the atlas maps in FLAT format with the //QuickNII //software
27 27  
28 28  (% start="3" %)
29 -1. (% style="color:#c0392b" %)**Anchored XML**(%%) file generated with the //QuickNII// software.
30 -1. (% style="color:#c0392b" %)**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). 
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). 
31 31  
32 32  [[image:Illustration seg_flat_files.png||height="254" width="500"]]
33 33