Configuration

To begin, open the Illumina Spatial Image Tool (ISIT) on your PC from the Start menu or desktop shortcut. Once the application launches, select Process images from the home screen to start the image processing workflow. You will then proceed to the Configuration page to enter the required microscope image details.

When entering the pixel size on the Illumina Spatial Image Tool, it is important to ensure that the pixel size is accurately entered within the range of 0.15 to 0.50 microns.

If you are using a slide scanner and do not know your pixel size, contact your Illumina Field Application Scientist (FAS) for assistance in obtaining your camera’s pixel size.

Note: Non-stitched images are not supported at this time.

Image processing is resource intensive, both in terms of RAM and CPU/GPU. While processing time is difficult to estimate, as it depends on a multitude of factors, the RAM requirement is straightforward: for every 1 GB of uncompressed image file size, 4 GB of free RAM is required. It is critical to use a computer with sufficient RAM installed (we recommend 32 GB of RAM) and to close unnecessary applications while using Illumina Spatial Image Tool.