Last modified by puchades on 2025/02/13 10:43
From version 61.1
edited by puchades
on 2025/02/13 10:33
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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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2 2  
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 -1. Remember to set your data proxy bucket to "public". Your collab can still be private.
6 6  1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
7 -1. Install DeepZoom, WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
6 +1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
8 8  
9 9  == How to install Collaboratory Apps ==
10 10  
11 11  1. To install Collaboratory Apps, click on the + Create button (top right corner).
12 12  1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
13 -1. Select the App to install (for example, DeepZoom), and click Save and View.
14 -1. Repeat this for all the relevant Community Apps. You will need, "DeepZoom"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
12 +1. Select the App to install (for example, WebAlign), and click Save and View.
13 +1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView".
15 15  1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
16 16  
17 -[[image:1739438141762-762.png||height="414" width="300"]]
18 -
19 19  == How to prepare your images? ==
20 20  
21 21  **~1. Prepare your images before upload by naming them according this naming convention:**
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28 28  
29 29  **2. Image ingestion**
30 30  
31 -Open the DeepZoom app and login with your EBRAINS credentials.
28 +Two alternatives are available, the QUINT image creator app, which is automatically creating the necessary files for downstream analyses in your collab. Or, you can use the image service app which is able to create image tiles in different formats. The steps for preparing your files are described bellow:
32 32  
30 +=== Use the "QUINT image creator" app ===
33 33  
34 -[[image:1739438392064-892.png]]
32 +**2a. Select images to ingest**
35 35  
36 -Select your bucket, the one where your images are stored.
34 +Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
37 37  
38 -Select the appropriate folder and click "Browse source" in order to visualise the images to ingest.
36 +The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
39 39  
40 -Enter the URL of the bucket by typing "/bucket_name/output_folder_name"
38 +When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
41 41  
42 -Press "Start process".
40 +Click on the "View Brain" button in order to preview your images.
43 43  
44 -By refreshing the status, you will see when the ingestion is completed.
42 +Now go to the WebAlign app in order to start the registration to atlas.
45 45  
46 -You now will have pyramid files in DZI format in your output folder. These can be opened by the WebAlign app.
44 +[[image:Screenshot create_brain app.png]]
47 47  
48 48  
49 -[[image:1739439061155-890.png]]
47 +=== Use Image service app (alt.) ===
50 50  
49 +**2b. Start the Image service UI from your webapp**
50 +
51 +* ** Fill in the requested information:**
52 +
53 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
54 +
55 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
56 +
57 + - you can filter the data using RegEx expressions. E.g. name_of_the_data_file.*\.jpg$ (for filtering jpeg files only). Or e.g hbp-00173_262_1366_1827.*\.tif$ for tiff files.
58 +
59 + - If your URL is valid, you will see the list of files by pressing "yes". Paste the name of the file you want to select. You can go back to the previous step  by pressing "back"
60 +
61 + - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
62 +
63 + - allow the image service to access your bucket
64 +
65 +[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
66 +
67 +- Store your results: Choose "create a new collab" where your ingested chunks will be stored in the bucket. This option is preferred in order not to overload the Bucket of your current  collab. Give a name to your Bucket as well as a name for the  collab (bucket slug) (see this illustration for more info)
68 +
69 +[[image:create collab.png]]
70 +
71 +- Customize your ingestion:
72 +
73 + - give a name to your ingestion in the "description of ingestion" field.
74 +
75 +* ** For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
76 +* ** Click //"preview"// in order to preview your task**
77 +* ** Click //"create task"//  to launch your ingestion**
78 +* ** Checking results in the Main UI page**
79 +
80 +Press "Task" in the higher right corner of the window.
81 +
82 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
83 +
84 +Otherwise, you will be redirected to the tasks list where the created task is selected.
85 +
86 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
87 +
88 +Refresh your browser in order to check the status of your task.
89 +
90 +When "successful", your chunks have been created.
91 +
51 51  == **How to use WebAlign** ==
52 52  
53 53  WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.  Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. The output of WebAlign can be used for analysis in the online QUINT workflow.
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188 188  
189 189  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.
190 190  
232 +
191 191  === Non-linear registration ===
192 192  
193 193  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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194 194  1. Select the waln file corresponding to your result from the WebAlign image registration.
195 195  1. Wait for the images to load: this may take some time.
196 196  
197 -[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
239 +[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
198 198  
199 199  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.
200 200  
201 - 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.
202 202  
203 203   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.
204 204  
205 205   6. Press Delete or Backspace to remove a marker under the mouse cursor.
206 206  
207 - 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.
208 208  
209 - 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”.
210 210  
211 -
212 212  
213 213  
214 214  == **How to use LocaliZoom** ==
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223 223  
224 224   A demo dataset is loaded using the file: demo_mouse_data_lz
225 225  
226 -=== Opening a private or EBRAINS dataset ===
227 227  
228 -LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
229 229  
230 -=== Create annotation points ===
267 +
231 231  
232 -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.
233 -
234 -Press "delete" in order to remove an annotation.
235 -
236 -Save your annotations with the "save" or "save as" buttons. The file format is .lz
237 -
238 -=== Export of coordinate points ===
239 -
240 -The created points can be exported to an Excel book by pressing "XLSX export".
241 -
242 -The saved .lz file can also be visualised in the 3D viewer, MeshView.
243 -
244 244  == **How to use MeshView** ==
245 245  
246 -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.
247 247  
248 -Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
249 -
250 -The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
251 -
252 -=== Open point cloud files ===
253 -
254 -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.
255 -
256 -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.
257 -
258 -Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
259 -
260 -=== Export images ===
261 -
262 -The "screenshot" button allows to capture the main window view as a png file.
263 -
264 -[[image:image19.png]]
265 -
266 266  
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