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 14.1
edited by puchades
on 2023/06/21 10:25
Change comment: There is no comment for this version

Summary

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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? ==
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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 33  **~1. Select images to ingest**
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41 41  Click on the "View Brain" button in order to preview your images.
42 42  
43 43  
43 +
44 44  
45 +== Use Image service app ==
45 45  
46 -== ==
47 +**~1. Start the Image service UI from your webapp**
47 47  
48 -=== Use Image service app ===
49 +**2. Fill in the requested information:**
49 49  
50 -**~1. Prepare your images before upload by naming them according this naming convention:**
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).
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