Attention: Data Proxy will be migrated from SWIFT to S3 storage at Friday, the 9th of May 2025 starting from 9pm CEST (my timezone). For more details, please join the rocket chat channel https://chat.ebrains.eu/channel/data-proxy-user-group


Last modified by puchades on 2025/02/13 10:43
From version 36.1
edited by puchades
on 2023/06/21 15:55
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, 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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222 222  
223 223  === Opening a private dataset ===
224 224  
224 +(% class="wikigeneratedid" %)
225 +All the .waln files located in the Bucket are displayed on the WebWarp main page. Your progress in WebWarp is saved as a .wwrp file.
226 +
227 +=== Opening an EBRAINS dataset ===
228 +
229 +If you would like to work with an EBRAINS dataset, open the LocaliZoom link from the KG dataset card ( [[https:~~/~~/search.kg.ebrains.eu>>url:https://search.kg.ebrains.eu]]) and paste it in the "Import LocaliZoom link" tab in WebAlign. Save this series as a .waln file you then can open in WebWarp.
230 +
231 +=== Non-linear registration ===
232 +
225 225  1. Navigate to the WebWarp app in the left-hand panel: all the .waln files located in the Bucket are displayed on the WebWarp main page.
226 226  1. Select the waln file corresponding to your result from the WebAlign image registration.
227 227  1. Wait for the images to load: this may take some time.
228 228  
229 -=== Opening an EBRAINS dataset ===
237 +[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
230 230  
231 -If you would like to work with an EBRAINS dataset, open the LocaliZoom link from the KG dataset card ( [[https:~~/~~/search.kg.ebrains.eu>>url:https://search.kg.ebrains.eu]]) and paste it in the "Import LocaliZoom link" tab in WebAlign. Save this series as a .waln file you then can open in WebWarp.
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.
232 232  
241 + 4. When going to “Settings”, the button for selecting the marker color will appear as well as “show triangles” which correspond to areas affected by the same    transformation.
233 233  
243 + 5. Place a marker on an area you want to stretch using the space bar. Nonlinear distortions are applied by dragging a marker using the mouse.
244 +
245 + 6. Press Delete or Backspace to remove a marker under the mouse cursor.
246 +
247 + 7. Save your results pression the “save” button. “Save as” will allow you to save the adjustments as a new file with a different name.
248 +
249 + 8. When the registration is finished, you can export your descriptor files ( .seg files used for analysis in the QUINT workflow) by pressing “export overlays”. All results are zipped and stored in the bucket. The result file name will be the same as the one chosen to create the registration, e.g. “my-registration.zip”.
250 +
251 +
252 +
253 +
234 234  == **How to use LocaliZoom** ==
235 235  
236 236  LocaliZoom is a web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases. LocaliZoom allows the viewing and exploring of high-resolution images with superimposed atlas overlays, and the extraction of coordinates of annotated points within those images for viewing in 3D brain atlas space.
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243 243  
244 244   A demo dataset is loaded using the file: demo_mouse_data_lz
245 245  
266 +=== Opening a private or EBRAINS dataset ===
246 246  
268 +LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
247 247  
248 -
270 +=== Create annotation points ===
249 249  
250 -== **How to use LocaliZoom** ==
272 +To extract a coordinate, the mouse marker must be positioned at the desired location, and press the space bar. A cross will appear in the selected colour (under Settings), representing the location of the extracted coordinate. After all desired points have been marked, the coordinates can be exported either to Excel.
251 251  
274 +Press "delete" in order to remove an annotation.
252 252  
276 +Save your annotations with the "save" or "save as" buttons. The file format is .lz
277 +
278 +=== Export of coordinate points ===
279 +
280 +The created points can be exported to an Excel book by pressing "XLSX export".
281 +
282 +The saved .lz file can also be visualised in the 3D viewer, MeshView.
283 +
284 +== **How to use MeshView** ==
285 +
286 +MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, and point clouds extracted from datasets.
287 +
288 +Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
289 +
290 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
291 +
292 +=== Open point cloud files ===
293 +
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.
295 +
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 +
304 +[[image:image19.png]]
305 +
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