spots not shown correctly for my Visium data

[zglu]

Dear Cirro Team,

Thanks again for the great tool and active support. I have one Visium data with ~500 spots and processed with Seurat. When I tried to visualize the data with cirro launch (1.1.54), the spots are not shown but only the image. Please see below a screenshot:

Below is what I expected to see with Seurat SpatialPlot() with option crop=F

It seems that the spot coordinates are incorrect in the data but I am not sure which slot cirro is using and how to incorporate the correct ones.

Many thanks for your support! Zhigang

[joshua-gould]

Can you please also share the h5ad or 10x h5 file as well? You can email it to cirrocumulus@googlegroups.com if you do not want to share it with Drive. Thanks.

[zglu]

Hi Josh, thanks a lot for your support. I will ask for permission from the data owner and then send you the files.

[joshua-gould]

Please note that you can subset the h5ad file to include only one gene as don’t need this part of the data to debug. Thanks

On Tue, May 30, 2023 at 4:40 PM Zhigang Lu @.***> wrote:

Hi Josh, thanks a lot for your support. I will ask for permission from the data owner and then send you the files.

— Reply to this email directly, view it on GitHub https://github.com/lilab-bcb/cirrocumulus/issues/193#issuecomment-1569067858, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABH6THZ54K4KZU2S4LYYNGTXIZLLLANCNFSM6AAAAAAYSL2NF4 . You are receiving this because you commented.Message ID: @.***>

[zglu]

Hi Josh, Thanks for the tip and your patience. I just figured it out that this happens when I split data of one section from a harmony-integrated object. When I use a single section data, the visualisation is normal.

Regarding this, what would be the best way to visualize an integrated object containing multiple sections? I am not sure how to concatenate the spatial images that match the integrated dataset.

Many thanks, Zhigang

[joshua-gould]

Please see the concat command - https://cirrocumulus.readthedocs.io/en/latest/commands.html#concatenate

On Thu, Jun 1, 2023 at 9:35 AM Zhigang Lu @.***> wrote:

Hi Josh, Thanks for the tip and your patience. I just figured it out that this happens when I split data of one section from a harmony-integrated object. When I use a single section data, the visualisation is normal.

Regarding this, what would be the best way to visualize an integrated object containing multiple sections? I am not sure how to concatenate the spatial images that match the integrated dataset.

Many thanks, Zhigang

— Reply to this email directly, view it on GitHub https://github.com/lilab-bcb/cirrocumulus/issues/193#issuecomment-1572066592, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABH6THZMRXWK2SECZN7YKA3XJCLDXANCNFSM6AAAAAAYSL2NF4 . You are receiving this because you commented.Message ID: @.***>