I followed the tutorial for Xenium data analysis with spatial trajectory inference to perform all analysis till clustering and start CCI gridding, but my H&E image is not aligned perfectly to the gridding.
Is this due to any mistakes from my image registration? How should I fix the issue?
I attached the gridding result below. [my registered h&e is too large to upload]
I followed the tutorial for Xenium data analysis with spatial trajectory inference to perform all analysis till clustering and start CCI gridding, but my H&E image is not aligned perfectly to the gridding.
Is this due to any mistakes from my image registration? How should I fix the issue?
I attached the gridding result below. [my registered h&e is too large to upload]
All the code follows tutorial and I am using 10x Adult Heart Xenium data. https://www.10xgenomics.com/datasets/human-heart-data-xenium-human-multi-tissue-and-cancer-panel-1-standard
For image registration, I am using 10x tutorial/step3. https://www.10xgenomics.com/analysis-guides/he-to-xenium-dapi-image-registration-with-fiji
Thank you for answering!