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1. Setting up the working environment - HBP Wiki
Attention: Data Proxy will be migrated from SWIFT to S3 storage at Friday, the 9th of May 2025 starting from 9pm CEST (my timezone). For more details, please join the rocket chat channel https://chat.ebrains.eu/channel/data-proxy-user-group


Last modified by puchades on 2025/02/13 10:43
From version 39.2
edited by puchades
on 2023/06/22 09:44
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To version 58.1
edited by puchades
on 2025/02/13 10:15
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.
5 5  1. Give users Admin, Editor or Viewer rights by clicking** Team** in the navigation panel.
6 -1. Install WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)
7 +1. Install DeepZoom, WebAlign, WebWarp, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)[[image:public_data_proxy_bucket.png]]
7 7  
8 8  == How to install Collaboratory Apps ==
9 9  
10 10  1. To install Collaboratory Apps, click on the + Create button (top right corner).
11 11  1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
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".
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".
14 14  1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.
15 15  
17 +[[image:1739438141762-762.png]]
18 +
16 16  == How to prepare your images? ==
17 17  
18 18  **~1. Prepare your images before upload by naming them according this naming convention:**
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25 25  
26 26  **2. Image ingestion**
27 27  
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:
31 +Use the DeepZoom app
29 29  
30 -=== Use the "QUINT image creator" app ===
31 -
32 -**2a. Select images to ingest**
33 -
34 34  Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
35 35  
36 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.
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41 41  
42 42  Now go to the WebAlign app in order to start the registration to atlas.
43 43  
44 -[[image:Screenshot create_brain app.png]]
45 45  
46 46  
47 -=== Use Image service app (alt.) ===
45 +
48 48  
49 -**2b. Start the Image service UI from your webapp**
47 +
50 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 -
92 92  == **How to use WebAlign** ==
93 93  
94 94  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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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.
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236 236  1. Select the waln file corresponding to your result from the WebAlign image registration.
237 237  1. Wait for the images to load: this may take some time.
238 238  
239 -[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
195 +[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
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.
199 + 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  
205 + 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  
207 + 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  
209 +
251 251  
252 252  
253 253  == **How to use LocaliZoom** ==
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262 262  
263 263   A demo dataset is loaded using the file: demo_mouse_data_lz
264 264  
224 +=== Opening a private or EBRAINS dataset ===
265 265  
226 +LocaliZoom will open all WebAlign (.waln) or WebWarp (.wwrp) files.
266 266  
267 -
228 +=== Create annotation points ===
268 268  
230 +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.
231 +
232 +Press "delete" in order to remove an annotation.
233 +
234 +Save your annotations with the "save" or "save as" buttons. The file format is .lz
235 +
236 +=== Export of coordinate points ===
237 +
238 +The created points can be exported to an Excel book by pressing "XLSX export".
239 +
240 +The saved .lz file can also be visualised in the 3D viewer, MeshView.
241 +
269 269  == **How to use MeshView** ==
270 270  
244 +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.
271 271  
246 +Online manual: [[https:~~/~~/meshview-for-brain-atlases.readthedocs.io/en/latest>>https://meshview-for-brain-atlases.readthedocs.io/en/latest]]
247 +
248 +The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
249 +
250 +=== Open point cloud files ===
251 +
252 +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.
253 +
254 +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.
255 +
256 +Navigation in the hierarchy is possible by clicking on the region names (grey boxes), this will collapse parts of the region tree.
257 +
258 +=== Export images ===
259 +
260 +The "screenshot" button allows to capture the main window view as a png file.
261 +
262 +[[image:image19.png]]
263 +
272 272  
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