Last modified by puchades on 2025/02/13 10:43
From version 31.1
edited by puchades
on 2023/06/21 11:25
Change comment: There is no comment for this version
To version 39.2
edited by puchades
on 2023/06/22 09:44
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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119 119  
120 120  [[image:create series webAlign.png]]
121 121  
122 -=== Opening a KG dataset ===
122 +=== Opening an EBRAINS dataset ===
123 123  
124 124  (% class="wikigeneratedid" %)
125 -If you would like to work with a KG dataset, fetch the LocaliZoom link from the KG dataset card and paste it in the "Import LocaliZoom link" tab.
125 +If you would like to work with an EBRAINS dataset, fetch the LocaliZoom link from the KG dataset card ( [[https:~~/~~/search.kg.ebrains.eu>>https://search.kg.ebrains.eu]] )and paste it in the "Import LocaliZoom link" tab.
126 126  
127 127  (% class="wikigeneratedid" %)
128 128  These series already have been registered to a reference atlas, so this gives you a starting point. The linear registrations obtained with WebAlign can be refined using WebWarp.
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206 206  
207 207  Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint).
208 208  
209 +== **How to use WebWarp** ==
209 209  
211 +WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases. Webwarp is compatible with registration performed with the WebAlign tool. Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system.
210 210  
211 -== **How to use WebAlign** ==
213 +Online user manual: [[https:~~/~~/webwarp.readthedocs.io/en/latest/>>https://webwarp.readthedocs.io/en/latest/]]
214 +
215 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
216 +
217 +=== Opening a sample dataset ===
218 +
219 +Demo dataset is loaded using the file: **demo_mouse_data.waln**
220 +
221 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.wwrp**
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 +
233 +=== Non-linear registration ===
234 +
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.
236 +1. Select the waln file corresponding to your result from the WebAlign image registration.
237 +1. Wait for the images to load: this may take some time.
238 +
239 +[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
240 +
241 +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.
242 +
243 + 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.
244 +
245 + 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.
246 +
247 + 6. Press Delete or Backspace to remove a marker under the mouse cursor.
248 +
249 +
250 +
251 +
252 +
253 +== **How to use LocaliZoom** ==
254 +
255 +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.
256 +
257 +Online Manual: [[https:~~/~~/localizoom.readthedocs.io/en/latest/>>https://localizoom.readthedocs.io/en/latest/]]
258 +
259 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
260 +
261 +=== Opening a sample dataset ===
262 +
263 + A demo dataset is loaded using the file: demo_mouse_data_lz
264 +
265 +
266 +
267 +
268 +
269 +== **How to use MeshView** ==
270 +
271 +
272 +
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