Last modified by puchades on 2025/02/13 10:43
From version 40.1
edited by puchades
on 2023/06/22 09:45
Change comment: There is no comment for this version
To version 53.1
edited by puchades
on 2023/07/05 09:25
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 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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29 29  
30 30  === Use the "QUINT image creator" app ===
31 31  
33 +(% 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".
34 +
32 32  **2a. Select images to ingest**
33 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.
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229 229  
230 230  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.
231 231  
232 -
233 233  === Non-linear registration ===
234 234  
235 235  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.
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265 265  
266 266   A demo dataset is loaded using the file: demo_mouse_data_lz
267 267  
270 +=== Opening a private or EBRAINS dataset ===
268 268  
272 +LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
269 269  
270 -
274 +=== Create annotation points ===
271 271  
276 +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.
277 +
278 +Press "delete" in order to remove an annotation.
279 +
280 +Save your annotations with the "save" or "save as" buttons. The file format is .lz
281 +
282 +=== Export of coordinate points ===
283 +
284 +The created points can be exported to an Excel book by pressing "XLSX export".
285 +
286 +The saved .lz file can also be visualised in the 3D viewer, MeshView.
287 +
272 272  == **How to use MeshView** ==
273 273  
290 +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.
274 274  
292 +Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
293 +
294 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
295 +
296 +=== Open point cloud files ===
297 +
298 +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.
299 +
300 +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.
301 +
302 +Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
303 +
304 +=== Export images ===
305 +
306 +The "screenshot" button allows to capture the main window view as a png file.
307 +
308 +[[image:image19.png]]
309 +
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