Last modified by puchades on 2025/02/13 10:43
From version 8.1
edited by puchades
on 2023/05/30 13:22
Change comment: There is no comment for this version
To version 10.1
edited by puchades
on 2023/06/21 10:22
Change comment: There is no comment for this version

Summary

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Content
... ... @@ -10,15 +10,149 @@
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 -== How to use Image service UI? ==
16 +== How to prepare your images? ==
17 17  
18 18  **~1. Prepare your images before upload by naming them according this naming convention:**
19 19  
20 20  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).
21 21  
22 +Example: tg2345_MMSH_s001.tif
23 +
24 +- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)
25 +
26 +**2. Image ingestion**
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:
29 +
30 +(% class="wikigeneratedid" %)
31 +=== ===
32 +
33 +=== Use the "QUINT image creator" app ===
34 +
35 +**~1. Select images to ingest**
36 +
37 +Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
38 +
39 +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 +
41 +When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
42 +
43 +Click on the "View Brain" button in order to preview your images.
44 +
45 +
46 +
47 +
48 +== ==
49 +
50 +=== Use Image service app ===
51 +
52 +**~1. Start the Image service UI from your webapp**
53 +
54 +**2. Fill in the requested information:**
55 +
56 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
57 +
58 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
59 +
60 + - 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.
61 +
62 + - 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"
63 +
64 + - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
65 +
66 + - allow the image service to access your bucket
67 +
68 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
69 +
70 +- 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)
71 +
72 +[[image:create collab.png||height="427" width="900"]]
73 +
74 +- Customize your ingestion:
75 +
76 + - give a name to your ingestion in the "description of ingestion" field.
77 +
78 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
79 +
80 +**4. Click //"preview"// in order to preview your task**
81 +
82 +**5. Click //"create task"//  to launch your ingestion**
83 +
84 +**6. Checking results in the Main UI page**
85 +
86 +Press "Task" in the higher right corner of the window.
87 +
88 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
89 +
90 +Otherwise, you will be redirected to the tasks list where the created task is selected.
91 +
92 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
93 +
94 +Refresh your browser in order to check the status of your task.
95 +
96 +When "successful", your chunks have been created.
97 +
98 +== ==
99 +
100 +=== Use Image service app ===
101 +
102 +**~1. Start the Image service UI from your webapp**
103 +
104 +**2. Fill in the requested information:**
105 +
106 + - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens.
107 +
108 +E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
109 +
110 + - 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.
111 +
112 + - 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"
113 +
114 + - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
115 +
116 + - allow the image service to access your bucket
117 +
118 +[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]
119 +
120 +- 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)
121 +
122 +[[image:create collab.png||height="427" width="900"]]
123 +
124 +- Customize your ingestion:
125 +
126 + - give a name to your ingestion in the "description of ingestion" field.
127 +
128 +**3. For obtaining chunks in DZI format  (compatible with WebAlign),** choose "2D" and "not stack of Images".
129 +
130 +**4. Click //"preview"// in order to preview your task**
131 +
132 +**5. Click //"create task"//  to launch your ingestion**
133 +
134 +**6. Checking results in the Main UI page**
135 +
136 +Press "Task" in the higher right corner of the window.
137 +
138 +When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.
139 +
140 +Otherwise, you will be redirected to the tasks list where the created task is selected.
141 +
142 +//Note! //A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"
143 +
144 +Refresh your browser in order to check the status of your task.
145 +
146 +When "successful", your chunks have been created.
147 +
148 +== ==
149 +
150 +=== Use Image service app ===
151 +
152 +**~1. Prepare your images before upload by naming them according this naming convention:**
153 +
154 +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).
155 +
22 22  Example: tg2345_MMSH_s001_segmentation.png
23 23  
24 24  - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//)