> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-stratamap/illumina-spatial-image-tool/image-processing/export-sample-files/ome-tiff.md).

# OME-TIFF

The output file from Illumina Spatial 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:

* Substrate ID: Identification of the substrate 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.


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