Changes for page QUINT demo collab

Last modified by puchades on 2023/10/18 15:44
From version 37.1
edited by sharoncy
on 2022/01/27 13:39
Change comment: There is no comment for this version
To version 67.2
edited by puchades
on 2023/03/14 09:51
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.
7 +This collab demonstrates a preliminary stage of integration of the QUINT workflow with the EBRAINS infrastructure.
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What is QUINT? =
15 +
16 16  
17 +{{box title="
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]].
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.
21 21  
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.
21 +**Contents**"}}
22 +{{toc/}}
23 +{{/box}}
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.
25 +== What is QUINT? ==
28 28  
27 +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 +
29 +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.
30 +
31 +* **[[Image Service:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Image%20Service]]** convert your image series to formats compatible with QUINT.
32 +* **[[WebAlign:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/WebAlign]] **enables registration of the 2D image series to a 3D reference atlas.
33 +* (% style="color:#16a085" %)**Webwarp**(%%) enables a nonlinear refinement of the WebAlign registration.
34 +* [[**webilastik:**>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik]] enables extraction of objects such as cells from the image series.
35 +* **[[NutilWeb:>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/NutilWeb]] **enables quantification of the extracted objects per atlas-region.
36 +* [[**Meshview: **>>https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/Meshview]]enables visualisation in 3D reference space.
37 +
38 +The apps may be used separately, or in sequence for full QUINT analysis. File transfer between the apps is done through the Bucket.
39 +
40 +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.
41 +
29 29  == Demo dataset ==
30 30  
31 -A demo dataset for use with the apps is provided in the Bucket: input and output files for all the tools are provided. The demo material originates from section images from the transgenic Arctic / Swedish mouse model of Alzheimer's disease that is available for download from the Human Brain Project Neuroinformatics Platform.
44 +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.
32 32  
33 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 34  
35 -= How to Install Collaboratory Apps =
48 +== How to Install Collaboratory Apps ==
36 36  
37 37  * For the purpose of this demo, the relevant apps have already been installed.
38 38  * 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/]].
39 39  
40 -= Who has access? =
53 +== Who has access? ==
41 41  
55 +* All collab users
42 42  * Collaboratory app developers
43 43  * Reviewers
44 44  
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45 45  
46 46  )))
47 47  
48 -
49 49  (% class="col-xs-12 col-sm-4" %)
50 50  (((
51 -{{box title="**Contents**"}}
52 -{{toc/}}
53 -{{/box}}
54 -
55 55  
56 56  )))
66 +
67 +* [[image:Collabs.quint.WebHome@QUINT_workflow_pic.png]]
57 57  )))
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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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