Last modified by puchades on 2021/11/16 09:11
From version 3.1
edited by puchades
on 2020/03/25 17:00
Change comment: Uploaded new attachment "Illustration seg_flat_files.png", version {1}
To version 1.4
edited by puchades
on 2020/03/24 09:59
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -5. Quantification and spatial analysis with Nutil
1 +6. Quantification and spatial analysis with Nutil
Content
... ... @@ -1,35 +1,30 @@
1 -== Nutil Quantifier ==
1 +== H2 Headings Will Appear in Table of Content ==
2 2  
3 -A detailed Nutil user manual is included when downloading the software.
4 4  
5 -**Basic steps:**
4 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
6 6  
7 -**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
6 +>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
8 8  
9 -(% start="1" style="list-style-type:decimal" %)
10 -1. **Segmentations with the labelling displayed in one RGB colour**
8 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
11 11  
12 -**Requirement:**
10 +=== H3 Headings Will Appear In The Table of Content ===
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//.
12 +==== You can also add images ====
17 17  
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.
14 +[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
19 19  
20 -(% start="2" %)
21 -1. **Customised anatomical atlas maps**
16 +Photo by David Clode
22 22  
23 -Generate the atlas maps in FLAT format with the //QuickNII //software
18 +==== Or code ====
24 24  
25 -(% start="3" %)
26 -1. **Anchored XML** file generated with the //QuickNII// software.
27 -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).
20 +Code blocks can be added by using the code macro:
28 28  
22 +{{code language="python"}}
23 +x = 1
24 +if x == 1:
25 + # indented four spaces
26 + print("x is 1.")
27 +{{/code}}
29 29  
30 -
31 -
32 -
33 -
34 34  (% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
35 35  
Illustration seg_flat_files.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -79.2 KB
Content