Attention: Due to an upgrade beginning on Friday, the 22nd August 2025, any new collabs, groups and any changes to teams will not be kept beyond the weekend. User creation will also be disabled during this time. The actual upgrade will take place on Wednesday, 27th August. On that day, any service requiring a Keycloak login will be unavailable for the duration of the upgrade. Thank you for your understanding as we complete this important work.

The Wiki service will be temporarily unavailable for scheduled maintenance on Friday, August 22nd, 2025, starting at 12:30 CEST up to 1H.

Following the system restart, the Collaboration and Group creation features will be temporarily disabled and will return HTTP 503 Service Unavailable errors until further notice.


Last modified by puchades on 2022/11/02 10:16
From version 45.1
edited by puchades
on 2020/09/23 13:26
Change comment: There is no comment for this version
To version 52.1
edited by puchades
on 2020/09/24 10:30
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,10 +1,13 @@
1 -(% style="text-align:center" %)
2 -[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
1 +[[image:QUINT_workflow_Plaques.png||style="float:left"]]
3 3  
4 -== (% style="color:#c0392b" %)**Workflow Description**(%%) ==
3 +== (% style="color:#c0392b" %)**Description**(%%) ==
5 5  
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:
5 +**The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. **
7 7  
7 +**Examples of use are: cell counting and spatial distributions; determination of projection areas in connectivity experiments; exploration of pathological hallmarks in brain disease models. Integration of various data to the same reference space enables new exploration strategies and re-use of experimental data.**
8 +
9 +The workflow is built on the following open access software:
10 +
8 8  * [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells, using machine learning image segmentation.
9 9  * [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates custom-angle slices from volumetric brain atlases to match the proportions and cutting plane of histological sections.
10 10  * //[[(% style="color:#3498db" %)VisuAlign>>doc:.Image registration to reference atlas using QuickNII.WebHome]]//(%%) is then used for nonlinear alignment of the reference atlas slice to the section image..
... ... @@ -12,7 +12,7 @@
12 12  
13 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.
14 14  
15 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
18 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
16 16  
17 17  
18 18  
... ... @@ -30,7 +30,7 @@
30 30  
31 31  QUINT workflow video
32 32  
33 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
36 +== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
34 34  
35 35  * The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
36 36  
QUINT_workflow_Plaques.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +213.7 KB
Content