Last modified by puchades on 2025/02/13 10:43
From version 55.1
edited by puchades
on 2025/02/13 10:01
Change comment: There is no comment for this version
To version 52.1
edited by puchades
on 2023/07/05 09:25
Change comment: Uploaded new attachment "public_data_proxy_bucket.png", version {1}

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2 2  
3 3  1. [[Register>>url:https://ebrains.eu/register/]] for an EBRAINS account, login, and set up a [[private collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/]].
4 4  1. Initialise the Bucket by clicking on Bucket in the navigation panel -> Create Bucket.
5 -1. Remember to set your data proxy bucket to "public". Your collab can still be private.
6 6  1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
7 -1. Install DeepZoom, WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
6 +1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
8 8  
9 9  == How to install Collaboratory Apps ==
10 10  
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26 26  
27 27  **2. Image ingestion**
28 28  
29 -Use the DeepZoom app
28 +Two alternatives are available, the QUINT image creator app, which is automatically creating the necessary files for downstream analyses in your collab. Or, you can use the image service app which is able to create image tiles in different formats. The steps for preparing your files are described bellow:
30 30  
31 -
30 +=== Use the "QUINT image creator" app ===
32 32  
32 +(% style="color:#e67e22" %)NB! we are still working on this app for the moment. For the enabling viewer links,  make your bucket "public". The collab can still be "private".
33 +
34 +**2a. Select images to ingest**
35 +
33 33  Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
34 34  
35 35  The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
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61 61  
62 62   - allow the image service to access your bucket
63 63  
64 -[[~[~[image:Skjermbilde 2022-02-08 103443.png~|~|height="199" width="500"~]~]>>attach:Skjermbilde 2022-02-08 103443.png]]
67 +[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
65 65  
66 66  - Store your results: Choose "create a new collab" where your ingested chunks will be stored in the bucket. This option is preferred in order not to overload the Bucket of your current  collab. Give a name to your Bucket as well as a name for the  collab (bucket slug) (see this illustration for more info)
67 67  
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234 234  1. Select the waln file corresponding to your result from the WebAlign image registration.
235 235  1. Wait for the images to load: this may take some time.
236 236  
237 -[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
240 +[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
238 238  
239 239  Your registered images are visible in the main window. The atlas regions with transparency sliders can be toggled using the “Atlas opacity” button. The color of the atlas outline can be modified by clicking on the colored rectangle.
240 240