Changes for page QUINT demo collab

Last modified by puchades on 2023/10/18 15:44
From version 38.1
edited by sharoncy
on 2022/01/27 13:42
Change comment: There is no comment for this version
To version 24.1
edited by sharoncy
on 2021/12/08 14:09
Change comment: There is no comment for this version

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15 15  = What is QUINT? =
16 16  
17 17  
18 -QUINT is an atlas-based workflow for quantification of cells and other features in 2-dimensional images of mouse or rat brain slices. For more information see[[ here>>https://ebrains.eu/service/quint]].
18 +QUINT is a workflow for atlas-based quantification of objects such as cells in 2D histological images from mouse or rat brain.
19 19  
20 -The online version of QUINT uses several applications installed from the EBRAINS Collaboratory App Store. These have been pre-installed in this collab and are displayed in the navigation panel (on the left-hand side in desktop browsers). Instructions for using the apps are also provided.
20 +The online version of QUINT uses several applications installed from the EBRAINS Collaboratory App Store. These have been pre-installed in this collab and are displayed in the panel in the top left corner. Instructions for using the apps are also provided.
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 -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 of the extracted objects per atlas-region.
25 -1. **Meshview: **enables visualisation in 3D reference space.
23 +1. **IlastikWeb:** 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.
26 26  
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.
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. The coordinates files can be viewed in Meshview. File transfer between the apps is done through the Collab Bucket.
28 28  
29 -== Demo datasets ==
30 30  
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 -
35 35  = How to Install Collaboratory Apps =
36 36  
37 37  * For the purpose of this demo, the relevant apps have already been installed.