OME-TIFF

The output file from Illumina StrataMap Image Tool is generated in the OME-TIFF format, which adheres strictly to the OME-TIFF standard. This file contains all the necessary images and data required for subsequent steps, detailed as follows:

Image Content

The OME-TIFF file includes three key images, each serving a specific purpose:

20x Registered Image (Pyramid Format)

• This image corresponds to your input image and retains the same resolution as the original.
• The image is stored in a pyramid format, which enables multi-resolution viewing. This ensures smooth navigation and visualization in spatial viewers or third-party image software.
• The pyramid storage allows for efficient rendering, especially for large, high-resolution images.

Tissue Mask

• This binary mask highlights the foreground (tissue) and background regions of the input image.
• The mask is edited as part of the Mask Editing Process and represents the final refined version.
• It is saved at a fixed resolution of 1 μm/pixel.

1 μm/pixel Image

• This image is an additional output at a standardized resolution of 1 μm/pixel, complementing the other data for downstream applications.

Metadata

The OME-TIFF file embeds comprehensive metadata required for downstream processing. This metadata is stored in the multi-value field, which can be viewed using any OME tag reader.

The metadata includes:

• Slide ID: Identification of the slide used.
• Sample IDs: Information about the individual samples included in the dataset.
• Image Version: Versioning details for the images in the file.
• Global Coordinates: Positional data for spatial alignment and mapping.

This structured and detailed format ensures compatibility with OME-compliant tools and facilitates smooth integration into workflows that require standardized image formats and metadata.