Changes for page QUINT demo collab

Last modified by puchades on 2023/10/18 15:44
From version 51.1
edited by sharoncy
on 2022/02/11 11:18
Change comment: There is no comment for this version
To version 63.1
edited by puchades
on 2022/09/30 15:44
Change comment: There is no comment for this version

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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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4 4  (((
5 5  = QUINT demo =
6 6  
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.
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.
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 +
16 +
17 +{{box title="**Contents**"}}
18 +{{toc/}}
19 +{{/box}}
20 +
15 15  == What is QUINT? ==
16 16  
17 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 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.
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.
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.
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 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.
26 26  
27 27  The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket.
28 28  
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41 41  
42 42  == Who has access? ==
43 43  
51 +* All collab users
44 44  * Collaboratory app developers
45 45  * Reviewers
46 46  
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47 47  
48 48  )))
49 49  
50 -
51 51  (% class="col-xs-12 col-sm-4" %)
52 52  (((
53 -{{box title="**Contents**"}}
54 -{{toc/}}
55 -{{/box}}
56 -
57 57  
58 58  )))
62 +
63 +*
59 59  )))
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1 -QUINT demo page for the report.
1 +QUINT demo page for setting up a working environemnt
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