Changes for page QUINT demo collab
Last modified by puchades on 2023/10/18 15:44
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... ... @@ -4,7 +4,7 @@ 4 4 ((( 5 5 = QUINT demo = 6 6 7 - demonstratesa preliminarystageofintegrationof theQUINT workflow with the EBRAINS infrastructure.Following usability improvementsand tighter integration of theworkflow components,QUINT will be publiclyreleased in Q3 2022.7 +This collab has been set up for demo of the online version of the QUINT workflow. 8 8 ))) 9 9 ))) 10 10 ... ... @@ -12,34 +12,27 @@ 12 12 ((( 13 13 (% class="col-xs-12 col-sm-8" %) 14 14 ((( 15 -= =What is QUINT? ==15 += What is QUINT? = 16 16 17 -QUINT is an atlas-based workflow for quantification of cells and other features in 2-dimensional images of mouse or rat brain sections. For more information see[[ here>>https://ebrains.eu/service/quint]]. 18 18 19 - The online version ofQUINTusesseveralapplicationsinstalledfrom the EBRAINS CollaboratoryApp Store.These have beenpre-installedinthiscollabandaredisplayedinthenavigationpanel(ontheleft-handsidein desktopbrowsers).Instructionsfor usingtheappsarelso provided.18 +QUINT is an atlas-based workflow for quantification of cells and other features in 2D images of mouse or rat brain slices. For more information see[[ here>>https://ebrains.eu/service/quint]]. 20 20 21 -1. **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT. 22 -1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas. 23 -1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series. 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: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space. 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 in desktop browsers, below on your mobile). Instructions for using the apps are also provided. 26 26 27 -The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket. 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. **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. 28 28 29 - As thefirststep, the imagestobeanalysedareuploadedto theBucket. The Image Serviceisused to convertthem toformatsthat are compatible with WebAlignand webilastik. Theresult of WebAlign andWebilastik are fed into NutilWeb, which generates reports,plots, overlayimages and coordinate files that can be downloaded from the Collab Bucket. The coordinates files may be viewed in Meshview.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. 30 30 31 -== Demo dataset == 32 32 33 - Ademodataset for usewiththe apps is providedinhe Bucket. The demo material originates from histologicalsection images from the transgenic Arctic / Swedish mousemodel ofAlzheimer'sdisease.30 += How to Install Collaboratory Apps = 34 34 35 -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 36 - 37 -== How to Install Collaboratory Apps == 38 - 39 39 * For the purpose of this demo, the relevant apps have already been installed. 40 40 * Instructions for setting up the working environment, which includes installation of the Collaboratory Apps, are provided [[here>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/How%20to%20install%20Collaboratory%20Apps/]]. 41 41 42 -= =Who has access? ==35 += Who has access? = 43 43 44 44 * Collaboratory app developers 45 45 * Reviewers