Last modified by puchades on 2025/02/13 10:43
From version 33.2
edited by puchades
on 2023/06/21 15:46
Change comment: There is no comment for this version
To version 41.2
edited by puchades
on 2023/06/22 09:56
Change comment: There is no comment for this version

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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 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)
6 +1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
7 7  
8 8  == How to install Collaboratory Apps ==
9 9  
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220 220  
221 221  You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
222 222  
223 +=== Opening a private dataset ===
224 +
225 +(% class="wikigeneratedid" %)
226 +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.
227 +
228 +=== Opening an EBRAINS dataset ===
229 +
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 +
232 +=== Non-linear registration ===
233 +
234 +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.
235 +1. Select the waln file corresponding to your result from the WebAlign image registration.
236 +1. Wait for the images to load: this may take some time.
237 +
238 +[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
239 +
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 +
242 + 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.
243 +
244 + 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.
245 +
246 + 6. Press Delete or Backspace to remove a marker under the mouse cursor.
247 +
248 + 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.
249 +
250 + 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”.
251 +
252 +
223 223  
254 +
255 +== **How to use LocaliZoom** ==
256 +
257 +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.
258 +
259 +Online Manual: [[https:~~/~~/localizoom.readthedocs.io/en/latest/>>https://localizoom.readthedocs.io/en/latest/]]
260 +
261 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
262 +
263 +=== Opening a sample dataset ===
264 +
265 + A demo dataset is loaded using the file: demo_mouse_data_lz
266 +
267 +=== Opening a private or EBRAINS dataset ===
268 +
269 +LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
270 +
271 +=== Create annotation points ===
272 +
273 +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** (XLSX export).
274 +
275 +Press delete in order to remove an annotation.
276 +
277 +=== Export of coordinate points ===
278 +
279 +or to **MeshView** (11) using the corresponding buttons in the upper toolbar.
280 +
281 +== **How to use MeshView** ==
282 +
283 +
284 +
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