Last modified by puchades on 2025/02/13 10:43
From version 46.1
edited by puchades
on 2023/06/22 13:23
Change comment: There is no comment for this version
To version 56.1
edited by puchades
on 2025/02/13 10:01
Change comment: There is no comment for this version

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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.
5 5  1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
6 -1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
7 +1. Install DeepZoom, WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
7 7  
8 8  == How to install Collaboratory Apps ==
9 9  
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10 10  1. To install Collaboratory Apps, click on the + Create button (top right corner).
11 11  1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
12 12  1. Select the App to install (for example, WebAlign), and click Save and View.
13 -1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
14 +1. Repeat this for all the relevant Community Apps. You will need, "DeepZoom"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
14 14  1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
15 15  
16 16  == How to prepare your images? ==
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25 25  
26 26  **2. Image ingestion**
27 27  
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:
29 +Use the DeepZoom app
29 29  
30 -=== Use the "QUINT image creator" app ===
31 +
31 31  
32 -**2a. Select images to ingest**
33 -
34 34  Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
35 35  
36 36  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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62 62  
63 63   - allow the image service to access your bucket
64 64  
65 -[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
64 +[[~[~[image:Skjermbilde 2022-02-08 103443.png~|~|height="199" width="500"~]~]>>attach:Skjermbilde 2022-02-08 103443.png]]
66 66  
67 67  - 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)
68 68  
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235 235  1. Select the waln file corresponding to your result from the WebAlign image registration.
236 236  1. Wait for the images to load: this may take some time.
237 237  
238 -[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
237 +[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
239 239  
240 240  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.
241 241  
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292 292  
293 293  === Open point cloud files ===
294 294  
295 -MeshView can open annotations from LocaliZoom (.lz files).
294 +MeshView can open annotations from LocaliZoom (.lz files). Possibility of a global control of all structures, using the slider will render the meshes transparent or disappear.
296 296  
296 +The individual control allow each structure to be made transparent or disappear. The color for each structure can be changed when clicking on the colored square.
297 +
298 +Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
299 +
300 +=== Export images ===
301 +
302 +The "screenshot" button allows to capture the main window view as a png file.
303 +
297 297  [[image:image19.png]]
305 +
306 +
public_data_proxy_bucket.png
Author
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1 +XWiki.puchades
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1 +14.4 KB
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