Changes for page QUINT demo collab

Last modified by puchades on 2023/10/18 15:44
From version 34.1
edited by sharoncy
on 2022/01/26 10:07
Change comment: There is no comment for this version
To version 38.1
edited by sharoncy
on 2022/01/27 13:42
Change comment: There is no comment for this version

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21 21  
22 22  1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a reference atlas.
23 23  1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells.
24 -1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification per atlas-region.
25 -1. **Meshview: **enables visualisation of the Nutil coordinate output.
24 +1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
25 +1. **Meshview: **enables visualisation in 3D reference space.
26 26  
27 -The apps may be used separately, or in sequence for full QUINT analysis. The output of WebAlign and IlastikWeb are fed into NutilWeb, which generates reports, images and coordinate files that can be downloaded from the Collab Bucket. The coordinates files may be viewed in Meshview. File transfer between the apps is done through the Bucket.
27 +The apps may be used separately, or in sequence for full QUINT analysis. The output of WebAlign and Webilastik are fed into NutilWeb, which generates reports, plots, overlay images and coordinate files that can be downloaded from the Collab Bucket. The coordinates files may be viewed in Meshview. File transfer between the apps is done through the Bucket.
28 28  
29 +== Demo datasets ==
29 29  
31 +Demo datasets for use with the apps are provided in the Bucket. The demo material originates from histological section images from the transgenic Arctic / Swedish mouse model of Alzheimer's disease.
32 +
33 +Lillehaug, S., Syverstad, G., Nilsson, L., Bjaalie, J. G., Leergaard, T. B., & Torp, R. (2018). //Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice// [Data set]. Human Brain Project Neuroinformatics Platform: https:~/~/doi.org/10.25493/G6CQ-D4D
34 +
30 30  = How to Install Collaboratory Apps =
31 31  
32 32  * For the purpose of this demo, the relevant apps have already been installed.