Select Tissue

In the Tissue selection page, the areas of interest on the tissue image are defined using a tissue image mask. A tissue mask is generated automatically and can be modified using the provided mask editing tool. Alternatively, a tissue mask can be imported if created using a third-party tool.

Auto-Generated Mask

Auto-generated masks are produced for all samples. By default, these masks are hidden until the user clicks the Apply Mask icon on the mask editor toolbar.

If the auto-generated masks are unsatisfactory, users can modify them using the built-in mask editor with the Add and Delete brushes.

Page Layout

The Tissue selection page consists of two panels:

1. Left panel: displays the list of samples.
2. Right panel: displays the mask editor.

Samples List

This panel shows the list of samples and their information, including:

1. Sample ID
2. Status: reviewed or not
3. Mask buffer setting

Clicking a row shows the selected sample. Clicking the Apply Mask icon on the right panel shows the auto-generated tissue mask.

Review of Tissue Mask

Reviewing a Sample

Initially, all samples will have the Reviewed status turned off. When a user confirms that the mask for a specific sample is satisfactory—whether using an auto-generated mask or an externally generated mask—the sample can be marked as Reviewed. This status is final, and no further changes will be allowed (the entire row will be disabled) unless you return to the previous step and reload the image.

Mask Buffer Setting

Tissue mask buffer extends the boundaries of the selected areas of interest on a mask. You can select a Small (20 μm), Medium (40 μm), or Large (60 μm) buffer boundary. After the buffer is set and the sample is marked Reviewed, Illumina Spatial Image Tool automatically enlarges these areas by the defined margin around the current tissue mask. See the medium buffer example screenshot below.

Reviewed Tissue mask with Medium buffer

Mask Editor

On the right panel is the mask editor, where the user can make modifications to the mask for the active sample. On its right-hand side are toolbar icons that the user can click to perform certain functions.

Icon	Description	Remarks
	Zoom in
	Zoom out
	Pan mode
	Apply/Unapply mask	Display the effect of applying the mask to the tissue image.
	"Add" brush	Brush for adding area of interest. The brush is a circle shape. Selected regions will show as a blue overlay.
	"Delete" brush	Brush for subtracting from area of interest. The brush is a circle shape.
	Download image	Downloads the tissue image to create a mask using a third-party tool.
	Upload external mask	Uploads a mask generated by a third-party tool into the mask editor, replacing the auto-generated mask.
	Delete/remove external mask	Removes the previously uploaded external mask and replaces it with the auto-generated mask.
	Reset	Revert all changes back to the original state, as if the Tissue selection page was just loaded for the first time.

These icons are enabled and disabled dynamically, depending on the state of the active/current sample. For example, when the current sample is in the Reviewed state, most of the icons will be disabled.

Brush Tool

When the Brush Tool is selected, the existing mask shows as blue, and regions can be added to the tissue area to be analyzed via the circle stamp.

See circle brush stamps added on the right

After checking Reviewed for all samples, click Next step to proceed.