Spatial Transcriptomics Spot Detector

A web tool for automatic spot detection and positional adjustments for spatial transcriptomics datasets.

The arrays used to generate ST datasets may contain positional variations due to printing artifacts. This web tool aims to detect correct spot positions using the images generated from the ST protocol. In order to obtain relevant experimental data, it is also possible to automatically select the spots which are located under the tissue, using a corresponding HE image. The spot positions and selections are further adjustable to one’s own needs.

The generated output file contains adjusted spot coordinates and pixel coordinates, together with a file containing a 3×3 affine matrix to transform array coordinates to pixel coordinates, which can be useful for downstream analysis.

The Spatial Transcriptomics Spot Detector is available at GitHub.

For questions regarding the software, please contact:

Kim Wong kim.wong@scilifelab.se
Jose Fernandez Navarro jose.fernandez.navarro@scilifelab.se