Author: Robina Afzal and Kevin Clare System: Digital Slide Archive (DSA)

This standard operating procedure describes how to create, label, and save annotations in the Digital Slide Archive. It also outlines the required naming conventions and the process for associating anatomical labels with UBERON ontology identifiers.

Request a Digital Slide Archive account by contacting:

1. Navigate to https://crarylabslides.com. 2. Log in using your DSA account. 3. Navigate through the Virtual Brain Bank to the appropriate folder. 4. Locate the slide that you have been assigned to annotate.

A number displayed on the slide thumbnail indicates how many annotation files are associated with that slide. For example, a thumbnail displaying the number 4 has four annotation files associated with it.

Figure 1. Example of a slide folder and thumbnail in the Virtual Brain Bank.

Click the desired slide file to open it in the DSA viewer.

Insert screenshot of the opened slide here.

Annotations associated with the slide are listed beneath the image.

Each annotation entry corresponds to a JSON file that may contain one or more annotation objects or regions. Annotation files can be:

* Downloaded * Added * Edited * Deleted

Open the annotation panel by clicking on 'Open in HistomicsUI' using the annotation control in the DSA viewer.

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Under the annotation panel, click New.

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A form will appear for creating a new annotation collection.

Use the following naming convention:

`ProjectName_AnnotatorInitials_Month_Year`

For example:

`YOLONeuropath_RA_July_2026`

The Name field in the form refers to the entire collection or set of annotations for that slide. All annotation objects created within this collection will be stored together in a single JSON file.

A single collection may contain multiple annotation types, such as:

• Gray matter
• White matter
• Leptomeninges
• Hippocampal regions
• Other assigned anatomical structures

The description must include:

* The types of structures being annotated * The project for whom the annotations are being created * The date the collection was created * The annotator’s full name * The annotator's level of training (novice, intermediate, advanced, pathologist)

Use the following format:

``` Annotation types: Gray matter, white matter, and leptomeninges Created for: Diana Date created: MM-DD-YYYY Annotator: Robina Afzal Training: Advanced ```

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1. Select Show on first load. 2. Click Save.

Selecting Show on first load ensures that the annotation collection is displayed automatically when the slide is opened.

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In the Draw panel, click the gear icon to open the annotation label settings.

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Click the plus sign under Name to create a new annotation label.

Enter the assigned anatomical structure or pathological entity (AB plaque, mature tangle…), such as:

`White Matter`

Each anatomical structure should be created as a separate annotation label.

Navigate to the EMBL-EBI Ontology Lookup Service:

https://www.ebi.ac.uk/ols4/ontologies/uberon

Search for the anatomical structure that you are annotating.

For example, a search for a structure may return an identifier such as:

`UBERON:0002020`

Use the Copy ID option on the ontology website to copy the identifier.

Insert screenshot of an example UBERON search here.

When a suitable UBERON term cannot be found, a new-term request may need to be submitted through the UBERON GitHub repository:

https://github.com/obophenotype/uberon/labels/new%20term%20request

The missing term must also be documented in the following tracking spreadsheet:

https://docs.google.com/spreadsheets/d/1bkEL8DL5_u71fHgqVKKwof1g5s7vyAp_lDZY8dNqEic/edit?usp=sharing

Until an official UBERON identifier is available, use a temporary identifier in the following format:

`UBERON:NA#`

Replace `#` with the assigned temporary number.

Enter the anatomical structure and UBERON identifier in the Name field.

Use the following format:

`Anatomical Structure UBERON:Identifier`

For example:

`Gray Matter UBERON:0002020`

Copy the complete contents of the Name field into the Label field.

The Name and Label fields should be identical.

Example:

```text Name: Gray Matter UBERON:0002020 Label: Gray Matter UBERON:0002020 ```

Optionally, select a different annotation line color to help distinguish the structure from other annotation labels.

1. Click Import. 2. Click Save.

Confirm that the new annotation label appears in the Draw panel.

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1. Confirm that the correct annotation label is selected. 2. Select the Line drawing tool.

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Always verify the selected label before beginning a new annotation.

Trace the boundary of the assigned anatomical region.

To create the annotation:

1. Click at multiple points along the boundary of the structure. 2. Continue placing points around the entire region. 3. Alternatively, hold down the input control and trace continuously when supported by the device. 4. Close or complete the annotation according to the DSA drawing-tool controls.

The annotation line will appear in the color assigned to the selected label.

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Repeat Steps 8–16 for every assigned anatomical structure.

Before tracing each structure, confirm that:

* The correct annotation label is selected. * The annotation name is spelled correctly. * The correct UBERON identifier is included. * The annotation is being added to the correct annotation collection. * The annotation boundary follows the intended anatomical structure.

Before completing the annotation session, verify that:

• The correct slide was selected.
• The annotation collection follows the required naming convention.
• The description includes the annotation types, project recipient, creation date, and annotator.
• Show on first load is selected.
• Each structure has its own annotation label.
• Each label contains the correct UBERON identifier.
• The Name and Label fields are identical.
• The correct label was selected before each region was traced.
• Annotation boundaries accurately follow the assigned anatomical structures.
• The annotation collection was saved successfully.