Last modified by puchades on 2025/02/13 10:43
From version 51.1
edited by puchades
on 2023/07/04 14:13
Change comment: There is no comment for this version
To version 40.1
edited by puchades
on 2023/06/22 09:45
Change comment: There is no comment for this version

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29 29  
30 30  === Use the "QUINT image creator" app ===
31 31  
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 34  **2a. Select images to ingest**
35 35  
36 36  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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231 231  
232 232  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.
233 233  
232 +
234 234  === Non-linear registration ===
235 235  
236 236  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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266 266  
267 267   A demo dataset is loaded using the file: demo_mouse_data_lz
268 268  
269 -=== Opening a private or EBRAINS dataset ===
270 270  
271 -LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
272 272  
273 -=== Create annotation points ===
270 +
274 274  
275 -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.
276 -
277 -Press "delete" in order to remove an annotation.
278 -
279 -Save your annotations with the "save" or "save as" buttons. The file format is .lz
280 -
281 -=== Export of coordinate points ===
282 -
283 -The created points can be exported to an Excel book by pressing "XLSX export".
284 -
285 -The saved .lz file can also be visualised in the 3D viewer, MeshView.
286 -
287 287  == **How to use MeshView** ==
288 288  
289 -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.
290 290  
291 -Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
292 -
293 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
294 -
295 -=== Open point cloud files ===
296 -
297 -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.
298 -
299 -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.
300 -
301 -Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
302 -
303 -=== Export images ===
304 -
305 -The "screenshot" button allows to capture the main window view as a png file.
306 -
307 -[[image:image19.png]]
308 -
309 309  
image19.png
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1 -XWiki.puchades
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