Post-Xenium Hematoxylin & Eosin (H&E) image segmentation

The XOA (Xenium Onboard Analysis) generated a DAPI image measuring 9679.38 x 7255.39 µm, and the corresponding post-Xenium H&E image has a size of 9229.43 x 6776.55 µm. Note that both DAPI and H&E images were acquired using a distinct microscopy system. Image registration was carried out to align both the DAPI and H&E images, followed by a 2D nucleus segmentation of the entire mouse brain using the StarDist algorithm. The mask was extracted and subsequently imported to filter transcripts within the mask/nuclei. However, an offset (right) occurred due to incomplete registration, which significantly reduced the number of transcripts in the downstream analysis as a result of this misalignment.

Source: In-house mouse brain sample