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 30.1
edited by puchades
on 2023/06/21 11:23
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 +40,17 @@
40 40  
41 41  Click on the "View Brain" button in order to preview your images.
42 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]]
44 44  
45 45  
46 -== ==
47 +=== Use Image service app (alt.) ===
47 47  
48 -=== Use Image service app ===
49 +**2b. Start the Image service UI from your webapp**
49 49  
50 -**~1. Prepare your images before upload by naming them according this naming convention:**
51 +* ** Fill in the requested information:**
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).
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"]]
65 +[[[[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"]]
69 +[[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".
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**
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.
... ... @@ -111,17 +111,17 @@
111 111  
112 112  === Opening a sample dataset ===
113 113  
114 -Demo dataset is loaded using the file: **demo_mouse_data_start**
102 +Demo dataset is loaded using the file: **demo_mouse_data_start.waln**
115 115  
116 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data**
104 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln**
117 117  
118 118  === Opening a private dataset ===
119 119  
120 -After you have uploaded your images to the bucket and ingested your images with the Image service, this has generated DZI chunks. These DZI files are used by WebAlign.
108 +After you have uploaded your images to the bucket and ingested your images with the QUINT Image creator app, this has generated DZIP chunks. These DZIP files are used by WebAlign.
121 121  
122 122  ~1. Start a new registration by pressing "create new series", the UI will ask you for the name of the collab where DZI chunks are stored. E.g. my-collab-name
123 123  
124 -2. WebAlign will search for DZI files and list those found.
112 +2. WebAlign will search for DZIP files and list those found.
125 125  
126 126  3. Enter a name for the descriptor json file which will be created and will contain your anchoring information.
127 127  
... ... @@ -129,6 +129,16 @@
129 129  
130 130  5. Press //"create"//. The main window will now display WebAlign. This step can take some time.
131 131  
120 +[[image:create series webAlign.png]]
121 +
122 +=== Opening a KG dataset ===
123 +
124 +(% class="wikigeneratedid" %)
125 +If you would like to work with a KG dataset, fetch the LocaliZoom link from the KG dataset card and paste it in the "Import LocaliZoom link" tab.
126 +
127 +(% class="wikigeneratedid" %)
128 +These series already have been registered to a reference atlas, so this gives you a starting point. The linear registrations obtained with WebAlign can be refined using WebWarp.
129 +
132 132  === Registration instructions ===
133 133  
134 134  **Short keys**
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
create series webAlign.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.puchades
Size
... ... @@ -1,0 +1,1 @@
1 +20.4 KB
Content