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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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241	241
242	242	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.
243	243
244		- 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	+ 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.
245	245
246	246	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.
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248	248	6. Press Delete or Backspace to remove a marker under the mouse cursor.
249	249
250		- 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.
251	251
252		- 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”.
253	253
254		-
255	255
256	256
257	257	== **How to use LocaliZoom** ==
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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 ===
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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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