Last modified by puchades on 2022/11/02 10:16
From version 8.1
edited by sharoncy
on 2020/03/09 13:53
Change comment: There is no comment for this version
To version 36.1
edited by sharoncy
on 2020/03/30 17:18
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,31 +1,47 @@
1 -
1 +(% style="text-align:center" %)
2 +[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
2 2  
3 -(% class="jumbotron" %)
4 -(((
5 -(% class="container" %)
6 -(((
7 -== QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain ==
8 -)))
9 -)))
4 +== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
10 10  
11 -(% class="row" %)
6 +The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software:
7 +
8 +1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
9 +1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) enables nonlinear adjustments of the reference atlas to the experimental section.
10 +1. (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of //ilastik// and //QuickNII//.
11 +
12 +In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
13 +
14 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
15 +
16 +
17 +
18 +
19 +
20 +
21 +
22 +
23 +
24 +
25 +==== ====
26 +
27 +
28 +
29 +
30 +
31 +==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
32 +
33 +* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
34 +
12 12  (((
13 -(% class="col-xs-12 col-sm-8" %)
14 -(((
15 -(% class="wikigeneratedid" %)
16 -
36 +* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
17 17  
18 -(% class="wikigeneratedid" id="H" %)
19 -The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software. The first – ilastik - allows the extraction of labelled features such as cells by segmentation. The second – QuickNII - generates atlas maps customised to match the proportions and cutting plane of the brain sections. The third – Nutil – enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII. In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
38 +==== (% style="color:#c0392b" %)**References**(%%) ====
20 20  
21 -= What can I find here? =
40 +Yates SC et al. 2019. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: 10.3389/fninf.2019.00075
22 22  
23 -* Notice how the table of contents on the right
24 -* is automatically updated
25 -* to hold this page's headers
42 +[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
26 26  
27 -= Who has access? =
44 +[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
28 28  
29 -Describe the audience of this collab.
46 +[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
30 30  )))
31 -)))
QUINT_workflow_pic.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +252.6 KB
Content
Youtube_QUINT.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +1.1 MB
Content
Collaboratory.Apps.Collab.Code.CollabClass[0]
Public
... ... @@ -1,1 +1,1 @@
1 -No
1 +Yes
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest
XWiki.XWikiRights[4]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view