Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Last modified by puchades on 2022/11/02 10:16
From version 2.1
edited by sharoncy
on 2020/03/09 13:03
Change comment: There is no comment for this version
To version 9.1
edited by sharoncy
on 2020/03/09 14:01
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,35 +1,26 @@
1 +
2 +
1 1  (% class="jumbotron" %)
2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= My Collab's Extended Title =
7 +== (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) ==
6 6  
7 -My collab's subtitle
9 +(% style="color:#999999" %)Neural Systems Laboratory, University of Oslo
8 8  )))
9 9  )))
10 10  
11 -(% class="row" %)
12 -(((
13 -(% class="col-xs-12 col-sm-8" %)
14 -(((
15 -= What can I find here? =
13 +==== ====
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
20 20  
21 -= Who has access? =
16 +==== (% style="color:#c0392b" %)Workflow Description(%%) ====
22 22  
23 -Describe the audience of this collab.
24 -)))
18 +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:
25 25  
20 +1. ilastik allows the extraction of labelled features such as cells by segmentation.
21 +1. QuickNII generates atlas maps customised to match the proportions and cutting plane of the brain sections.
22 +1. Nutil enables quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.
26 26  
27 -(% class="col-xs-12 col-sm-4" %)
28 -(((
29 -{{box title="**Contents**"}}
30 -{{toc/}}
31 -{{/box}}
24 +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.
32 32  
33 33  
34 -)))
35 -)))
XWiki.XWikiRights[1]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +Collabs.quint._.groups.collab-quint-editor
Levels
... ... @@ -1,0 +1,1 @@
1 +view,comment,edit
XWiki.XWikiRights[2]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +Collabs.quint._.groups.collab-quint-administrator
Levels
... ... @@ -1,0 +1,1 @@
1 +view,comment,edit,delete