Changes for page QUINT demo collab
Last modified by puchades on 2023/10/18 15:44
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... ... @@ -1,1 +1,1 @@ 1 -QUINT demo 1 +QUINT demo collab - Author
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... ... @@ -4,9 +4,7 @@ 4 4 ((( 5 5 = QUINT demo = 6 6 7 -This collab has been set up for demo of the online version of the QUINT workflow. 8 - 9 -The current integration level is basic and will improve during the remaining SGA3 period. 7 +This collab demonstrates a preliminary stage of integration of the QUINT workflow with the EBRAINS infrastructure. Following usability improvements and tighter integration of the workflow components, QUINT will be publicly released in Q3 2022. 10 10 ))) 11 11 ))) 12 12 ... ... @@ -14,23 +14,29 @@ 14 14 ((( 15 15 (% class="col-xs-12 col-sm-8" %) 16 16 ((( 17 - ==What is QUINT? ==15 + 18 18 19 -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]]. 17 +{{box title="**Contents**"}} 18 +{{toc/}} 19 +{{/box}} 20 20 21 - Theonline versionofQUINTuses 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.21 +== What is QUINT? == 22 22 23 -1. **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT. 24 -1. **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas. 25 -1. [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series. 26 -1. **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region. 27 -1. [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space. 23 +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]]. 28 28 25 +The web 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. 29 29 30 -The apps may be used separately, or in sequence for full QUINT analysis. 27 +* **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT. 28 +* **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas. 29 +* **[[LocaliZoom>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/How%20to%20perform%20a%20nonlinear%20registration%20with%20LocaliZoom/]]** enables a nonlinear refinement of the WebAlign registration. 30 +* [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series. 31 +* **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region. 32 +* [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space. 31 31 32 -The Image Service isused to convert the imagesto formats that are compatiblewith WebAlign andwebilastik. Theoutput of WebAlignand Webilastik are fed into NutilWeb, which generates reports, plots, overlayimages andcoordinatefiles that canbedownloadedfromthe CollabBucket.Thecoordinates files maybe viewed in Meshview.34 +The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket. 33 33 36 +As the first step, the images to be analysed are uploaded to the Bucket. The Image Service is used to convert them to formats that are compatible with WebAlign and webilastik. The result 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. 37 + 34 34 == Demo dataset == 35 35 36 36 A demo dataset for use with the apps is provided in the Bucket. The demo material originates from histological section images from the transgenic Arctic / Swedish mouse model of Alzheimer's disease. ... ... @@ -44,6 +44,7 @@ 44 44 45 45 == Who has access? == 46 46 51 +* All collab users 47 47 * Collaboratory app developers 48 48 * Reviewers 49 49 ... ... @@ -50,13 +50,10 @@ 50 50 51 51 ))) 52 52 53 - 54 54 (% class="col-xs-12 col-sm-4" %) 55 55 ((( 56 -{{box title="**Contents**"}} 57 -{{toc/}} 58 -{{/box}} 59 - 60 60 61 61 ))) 62 + 63 +* 62 62 )))
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