Overlaying H&E stained images with CosMx data

[gohantsubu]

Hello,

Thank you for developing such an effective tool. I am a researcher just starting spatial transcriptomics analysis with CosMx. I have successfully uploaded my CosMx h5ad data into Cirrocumulus, which has been very helpful. I would now like to overlay this data with H&E-stained images. Could you please guide me through the steps to achieve this?

Best regards,
Hirotaka Inoue

[joshua-gould]

You need to rename your H&E image to correspond to the naming that cirrocumulus expects. The --spatial argument currently takes "Directory containing 10x visium spatial data (tissue_hires_image.png, scalefactors_json.json, and tissue_positions_list.csv) or a directory containing image.png, positions.image.csv with headers barcode, x, and y, and optionally diameter.image.txt containing spot diameter"

[gohantsubu]

Thank you for your reply. I will start by modifying our H&E data as suggested.

[gohantsubu]

Thank you for your reply. I tried the solution you suggested with a single FOV. I uploaded the HE image as image.png and the X, Y coordinate data as positions.image.csv. This created an "image" tab under the embeddings section, so the upload seemed to be successful. However, as shown in the snapshot, all the plots are clustered in the top-left corner. I suspect this is because the coordinate scale is incorrect. Could you please advise on how to resolve this?

Best regards,
Hirotaka Inoue

[gohantsubu]

Thank you for all your help.
We are sorry to bother you, but we are looking forward to your reply to our question.

Best regards,
Hirotaka Inoue