Changes for page 1. Setting up the working environment
Last modified by puchades on 2025/02/13 10:43
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... ... @@ -229,7 +229,6 @@ 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. ... ... @@ -240,14 +240,17 @@ 240 240 241 241 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. 242 242 243 - 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. 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. 244 244 245 245 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. 246 246 247 247 6. Press Delete or Backspace to remove a marker under the mouse cursor. 248 248 248 + 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. 249 249 250 + 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”. 250 250 252 + 251 251 252 252 253 253 == **How to use LocaliZoom** == ... ... @@ -262,10 +262,20 @@ 262 262 263 263 A demo dataset is loaded using the file: demo_mouse_data_lz 264 264 267 +=== Opening a private or EBRAINS dataset === 265 265 269 +LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files. 266 266 267 - 271 +=== Create annotation points === 268 268 273 +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 + 269 269 == **How to use MeshView** == 270 270 271 271