To set up the working environment:

1. Register for an EBRAINS account, login, and set up a private collab.
2. Initialise the Bucket by clicking on Bucket in the navigation panel -> Create Bucket.
3. Give users Admin, Editor or Viewer rights by clicking Team in the navigation panel.
4. Install WebAlign, LocaliZoom, and Meshview from the EBRAINS Collaboratory App Store (see instructions below)

How to install Collaboratory Apps

1. To install Collaboratory Apps, click on the + Create button (top right corner). 
2. Give the page a Title (for example, WebAlign), select the Community App option, and click Create.
3. Select the App to install (for example, WebAlign), and click Save and View.
4. Repeat this for all the relevant Community Apps.
5. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket.

How to use Image service UI?

1. Prepare your images before upload by naming them according this naming convention:

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).

Example: tg2345_MMSH_s001_segmentation.png

- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on "Bucket")

2. Start the Image service UI from your webapp

3. Fill in the requested information:

  - type or paste the URL of the dataset folder containing the images. Note! the name of the collab supports only hyphens.

E.g. https://data-proxy.ebrains.eu/api/buckets/name-of-my-collab

 - you can filter the data using RegEx expressions. E.g. name_of_the_data_folder\/.*\.jpg$ (for filtering jpeg files only).

 - 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"

 - Or use a prefix: E.g. https://data-proxy.ebrains.eu/api/buckets/name-of-my-collab?prefix=name_of_the_data_folder

 - allow the image service to access your bucket

- 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)

- Customize your ingestion:

       - give a name to your ingestion in the "description of ingestion" field.

3. For obtaining chunks in DZI format  (compatible with WebAlign), choose "2D" and "not stack of Images".

4. Click "preview" in order to preview your task

5. Click "create task"  to launch your ingestion

6. Checking results in the Main UI page

Press "Task" in the higher right corner of the window.

When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance.

Otherwise, you will be redirected to the tasks list where the created task is selected.

Note! A task will be first "Queued" then "Running"; "Stagingout"and ultimately "Successful" or "Failed"

Refresh your browser in order to check the status of your task.

When "successful", your chunks have been created.