Changes for page QUINT demo collab

Last modified by puchades on 2023/10/18 15:44
From version 49.1
edited by sharoncy
on 2022/02/08 15:53
Change comment: There is no comment for this version
To version 70.1
edited by puchades
on 2023/10/18 15:42
Change comment: There is no comment for this version

Summary

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Title
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1 -QUINT demo
1 +QUINT demo collab
Author
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1 -XWiki.sharoncy
1 +XWiki.puchades
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= QUINT demo =
5 += QUINT online 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.
10 10  )))
11 11  )))
12 12  
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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="
20 20  
21 -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.
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.
20 +**Contents**"}}
21 +{{toc/}}
22 +{{/box}}
28 28  
24 +== What is QUINT? ==
29 29  
30 -The apps may be used separately, or in sequence for full QUINT analysis.
26 +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]].
31 31  
32 -The Image Service is used to convert the images to formats that are compatible with WebAlign and webilastik. 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 +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.
33 33  
30 +* **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT.
31 +* **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas.
32 +* [[(% style="color:#16a085" %)**Webwarp**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebWarp]](%%) enables a nonlinear refinement of the WebAlign registration.
33 +* [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series.
34 +* **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
35 +* [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space.
36 +
37 +The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket.
38 +
39 +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.
40 +
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.
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44 44  
45 45  == Who has access? ==
46 46  
54 +* All collab users
47 47  * Collaboratory app developers
48 48  * Reviewers
49 49  
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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  )))
65 +
66 +*
62 62  )))
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1 -QUINT demo page for the report.
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