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 36.2
edited by puchades
on 2020/04/07 15:38
Change comment: There is no comment for this version
To version 45.2
edited by puchades
on 2020/09/23 13:27
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,6 +1,7 @@
1 1  (% style="text-align:center" %)
2 2  [[image:QUINT_workflow_pic.png||height="394" width="1011"]]
3 3  
4 +
4 4  == (% style="color:#c0392b" %)**Workflow Description**(%%) ==
5 5  
6 6  The QUINT workflow facilitates the quantification and spatial analysis of labelled features in images of histological sections from the rodent brain using 3D reference atlases. The workflow is built on the following open access software:
... ... @@ -23,15 +23,16 @@
23 23  
24 24  
25 25  
26 -==== ====
27 27  
28 28  
29 29  
30 30  
31 31  
32 +QUINT workflow video
33 +
32 32  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
33 33  
34 -* The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.
36 +* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
35 35  
36 36  (((
37 37  * As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
... ... @@ -38,11 +38,10 @@
38 38  
39 39  ==== (% style="color:#c0392b" %)**References**(%%) ====
40 40  
41 -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
42 -
43 -[[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
44 -
45 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
46 -
47 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
43 +* 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>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
44 +* Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: 10.3389/fninf.2020.00037
45 +* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
46 +* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
47 +* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
48 +* [[ilastik>>https://www.ilastik.org/]]
48 48  )))
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest
XWiki.XWikiRights[4]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiAllGroup
Levels
... ... @@ -1,1 +1,0 @@
1 -view
XWiki.XWikiRights[5]
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[6]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view