Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time

Warning: The EBRAINS Drive and EBRAINS Lab will down on Tuesday, the 8th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour.


Last modified by puchades on 2025/02/13 10:43
From version 8.2
edited by puchades
on 2023/06/21 10:18
Change comment: There is no comment for this version
To version 23.1
edited by puchades
on 2023/06/21 10:56
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -10,7 +10,7 @@
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 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.
13 +1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "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  
16 16  == How to prepare your images? ==
... ... @@ -21,18 +21,17 @@
21 21  
22 22  Example: tg2345_MMSH_s001.tif
23 23  
24 +- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
25 +
24 24  **2. Image ingestion**
25 25  
26 26  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:
27 27  
28 -(% class="wikigeneratedid" %)
29 -=== ===
30 -
31 31  === Use the "QUINT image creator" app ===
32 32  
33 -**~1. Select images to ingest**
32 +**2a. Select images to ingest**
34 34  
35 -Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
34 +Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
36 36  
37 37  The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
38 38  
... ... @@ -40,25 +40,15 @@
40 40  
41 41  Click on the "View Brain" button in order to preview your images.
42 42  
42 +[[image:Screenshot create_brain app.png]]
43 43  
44 44  
45 -
46 -== ==
47 -
48 48  === Use Image service app ===
49 49  
50 -**~1. Prepare your images before upload by naming them according this naming convention:**
47 +**2b. Start the Image service UI from your webapp**
51 51  
52 -The ID should be unique to the particular brain section and in the format sXXX, with XXX representing the section number. The section number should reflect the serial order and spacing of the sections (e.g., s002, s006, s010 for every 4^^th^^ section starting with section 2).
49 +* ** Fill in the requested information:**
53 53  
54 -Example: tg2345_MMSH_s001_segmentation.png
55 -
56 -- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
57 -
58 -**2. Start the Image service UI from your webapp**
59 -
60 -**3. Fill in the requested information:**
61 -
62 62   - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
63 63  
64 64  E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
... ... @@ -71,24 +71,21 @@
71 71  
72 72   - allow the image service to access your bucket
73 73  
74 -[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
63 +[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]]
75 75  
76 76  - 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)
77 77  
78 -[[image:create collab.png||height="427" width="900"]]
67 +[[image:create collab.png]]
79 79  
80 80  - Customize your ingestion:
81 81  
82 82   - give a name to your ingestion in the "description of ingestion" field.
83 83  
84 -**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
73 +* ** For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
74 +* ** Click //"preview"// in order to preview your task**
75 +* ** Click //"create task"//  to launch your ingestion**
76 +* ** Checking results in the Main UI page**
85 85  
86 -**4. Click //"preview"// in order to preview your task**
87 -
88 -**5. Click //"create task"//  to launch your ingestion**
89 -
90 -**6. Checking results in the Main UI page**
91 -
92 92  Press "Task" in the higher right corner of the window.
93 93  
94 94  When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
Screenshot create_brain app.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +62.6 KB
Content
Skjermbilde 2022-02-08 103443.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +13.8 KB
Content
create collab.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +283.8 KB
Content