Changes for page 1. Setting up the working environment

Last modified by puchades on 2025/02/13 10:43

From 39.1 to 38.1 From 52.1 to 51.1

From version 51.1

edited by puchades
on 2023/07/04 14:13

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To version 39.1

edited by puchades
on 2023/06/22 09:40

Change comment: Uploaded new attachment "image1.png", version {1}

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- image19.png

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@@ -29,8 +29,6 @@
  === Use the "QUINT image creator" app ===
--(% 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".
--
  **2a. Select images to ingest**
  Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
@@ -224,36 +224,15 @@
  === Opening a private dataset ===
--(% class="wikigeneratedid" %)
--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.
--
--=== Opening an EBRAINS dataset ===
--
--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.
--
--=== Non-linear registration ===
--
 . 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.
 . Select the waln file corresponding to your result from the WebAlign image registration.
 . Wait for the images to load: this may take some time.
--[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
++=== Opening an EBRAINS dataset ===
--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.
++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.
--     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.
--     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.
--
--     6. Press Delete or Backspace to remove a marker under the mouse cursor.
--
--     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.
--
--     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”.
--
--
--
--
  == **How to use LocaliZoom** ==
  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.
@@ -266,44 +266,11 @@
   A demo dataset is loaded using the file: demo_mouse_data_lz
--=== Opening a private or EBRAINS dataset ===
--LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
--=== Create annotation points ===
++
--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.
--
--Press "delete" in order to remove an annotation.
--
--Save your annotations with the "save" or "save as" buttons. The file format is .lz
--
--=== Export of coordinate points ===
--
--The created points can be exported to an Excel book by pressing "XLSX export".
--
--The saved .lz file can also be visualised in the 3D viewer, MeshView.
--
  == **How to use MeshView** ==
--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.
--Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
--
--The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
--
--=== Open point cloud files ===
--
--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.
--
--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.
--
--Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
--
--=== Export images ===
--
--The "screenshot" button allows to capture the main window view as a png file.
--
--[[image:image19.png]]
--