Warning:  Due to planned infrastructure maintenance, the EBRAINS Wiki and EBRAINS Support system will be unavailable for up to three days starting Monday, 14 July. During this period, both services will be inaccessible, and any emails sent to the support address will not be received.

Attention: The EBRAINS Chat will down on Thursday, the 10th of July 2025 starting from 18.00pm CEST (my timezone) for up to 1 hour. 

Warning: The EBRAINS Drive, EBRAINS Bucket and EBRAINS Lab will down today, Wednesday, the 9th of July 2025 starting from 19:30 CEST (my timezone) for up to 1 hour.


Last modified by puchades on 2022/11/02 10:16
From version 28.2
edited by puchades
on 2020/03/12 16:50
Change comment: There is no comment for this version
To version 7.1
edited by sharoncy
on 2020/03/09 13:46
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
... ... @@ -1,34 +1,34 @@
1 -(% style="text-align:center" %)
2 -[[image:QUINT_workflow_pic.png]]
1 +
3 3  
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 4  
5 -==== (% style="color:#c0392b" %)**Workflow Description**(%%) ====
11 +(% class="row" %)
12 +(((
13 +(% class="col-xs-12 col-sm-8" %)
14 +(((
15 +(% class="wikigeneratedid" %)
16 += =
6 6  
7 -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:
18 += What can I find here? =
8 8  
9 -1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation.
10 -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.
11 -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.
20 +* Notice how the table of contents on the right
21 +* is automatically updated
22 +* to hold this page's headers
12 12  
13 -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.
24 += Who has access? =
14 14  
15 -[[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
26 +Describe the audience of this collab.
27 +)))
16 16  
17 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
18 18  
19 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
20 -
30 +(% class="col-xs-12 col-sm-4" %)
21 21  (((
22 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
23 -
24 -==== (% style="color:#c0392b" %)**References**(%%) ====
25 -
26 -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
27 -
28 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
29 -
30 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
31 -
32 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
32 +
33 33  )))
34 -
34 +)))
QUINT_workflow_pic.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.puchades
Size
... ... @@ -1,1 +1,0 @@
1 -252.6 KB
Content