Can I use the tissue_hires_image.png as the input of step0?

[yuu342]

Hello,I just get tissue_hires_image.png and I don't have the tif format. Can I use the tissue_hires_image.png as the input of step0?

[LingyuLi-math]

Hi,

Thanks for your question.

Just to clarify, tissue_hires_image.png is a Space Ranger output, not the original input histology image.
The original input for Space Ranger is usually a high-resolution tissue image (e.g., TIF), and Space Ranger generates tissue_hires_image.png together with the spatial metadata.

For FineST Step_0, the most important requirement is that the histology image coordinates are correctly aligned with the spatial RNA-seq coordinates.
Specifically, the spot locations should correspond to the image pixel coordinates after applying the scale factor from scalefactors_json.json (e.g., spot_diameter_fullres ), matching the coordinates in adata.obsm['spatial'].

Therefore, if you only have tissue_hires_image.png, you can try using it as input, but the scaled-down image may result in the loss of some cell-morphology information. Please make sure that:

• The image coordinates are consistent with the spatial coordinates in your AnnData object.
• The corresponding scalefactors_json.json is available so that the spot/image alignment can be correctly handled.

If you still have access to the original high-resolution histology image used for Space Ranger, I recommend using it instead, as it preserves more cell-morphology detail for patch extraction.

Best,
Lingyu Li