Last modified by puchades on 2025/02/13 10:43
From version 51.1
edited by puchades
on 2023/07/04 14:13
Change comment: There is no comment for this version
To version 61.1
edited by puchades
on 2025/02/13 10:33
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||height="414" width="300"]]
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 +Open the DeepZoom app and login with your EBRAINS credentials.
29 29  
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".
34 +[[image:1739438392064-892.png]]
33 33  
34 -**2a. Select images to ingest**
36 +Select your bucket, the one where your images are stored.
35 35  
36 -Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
38 +Select the appropriate folder and click "Browse source" in order to visualise the images to ingest.
37 37  
38 -The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
40 +Enter the URL of the bucket by typing "/bucket_name/output_folder_name"
39 39  
40 -When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
42 +Press "Start process".
41 41  
42 -Click on the "View Brain" button in order to preview your images.
44 +By refreshing the status, you will see when the ingestion is completed.
43 43  
44 -Now go to the WebAlign app in order to start the registration to atlas.
46 +You now will have pyramid files in DZI format in your output folder. These can be opened by the WebAlign app.
45 45  
46 -[[image:Screenshot create_brain app.png]]
47 47  
49 +[[image:1739439061155-890.png]]
48 48  
49 -=== Use Image service app (alt.) ===
50 -
51 -**2b. Start the Image service UI from your webapp**
52 -
53 -* ** Fill in the requested information:**
54 -
55 - - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
56 -
57 -E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
58 -
59 - - 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.
60 -
61 - - 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"
62 -
63 - - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
64 -
65 - - allow the image service to access your bucket
66 -
67 -[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
68 -
69 -- 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)
70 -
71 -[[image:create collab.png]]
72 -
73 -- Customize your ingestion:
74 -
75 - - give a name to your ingestion in the "description of ingestion" field.
76 -
77 -* ** For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
78 -* ** Click //"preview"// in order to preview your task**
79 -* ** Click //"create task"//  to launch your ingestion**
80 -* ** Checking results in the Main UI page**
81 -
82 -Press "Task" in the higher right corner of the window.
83 -
84 -When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
85 -
86 -Otherwise, you will be redirected to the tasks list where the created task is selected.
87 -
88 -//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
89 -
90 -Refresh your browser in order to check the status of your task.
91 -
92 -When "successful", your chunks have been created.
93 -
94 94  == **How to use WebAlign** ==
95 95  
96 96  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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237 237  1. Select the waln file corresponding to your result from the WebAlign image registration.
238 238  1. Wait for the images to load: this may take some time.
239 239  
240 -[[[[image:image1.png||alt="_images/image1.png"]]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
197 +[[~[~[image:image1.png~|~|alt="_images/image1.png"~]~]>>url:https://webwarp.readthedocs.io/en/latest/_images/image1.png]]
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  
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