display multiple Visium datasets on top of H&E images

[zglu]

Hello Cirro team, Does Cirro currently support displaying multiple Visium datasets (from different sections), each on top of an H&E image? (such as below an example from cellxgene)

Thanks, Zhigang

[joshua-gould]

Please see https://cirrocumulus.readthedocs.io/en/latest/commands.html#concatenate

[zglu]

Thanks for the rapid development of the function. I tried with the following command but got an error: cirro concat --output MouseBrain_concat/ V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain.h5ad V1_Mouse_Brain_Sagittal_Posterior/V1_Mouse_Brain_post_sct.h5ad

Traceback (most recent call last): File "/Users/zlu/miniconda3/bin/cirro", line 5, in from cirrocumulus.main import main File "/Users/zlu/miniconda3/lib/python3.7/site-packages/cirrocumulus/main.py", line 6, in from cirrocumulus import concat, launch, prepare_data, serve File "/Users/zlu/miniconda3/lib/python3.7/site-packages/cirrocumulus/concat.py", line 12, in def concat_spatial(paths: list[str], output_dir: str, ncols: int = 2): TypeError: 'type' object is not subscriptable

What can be the problem please?

[joshua-gould]

There was a bug parsing the command line arguments. Can you please update to the latest version and try again? Also, can you please use Python 3.9 or later too? Thanks.

[zglu]

Hi Joshua,

I've updated Python to 3.10 and installed the latest version of Cirro. Now the concat function works. But it seems that the row and col values in the data were swapped while the images were unchanged. For a single dataset it works in the same way. Maybe need to fix something..

Many thanks, Zhigang

[joshua-gould]

Thanks for your reply. I'm not sure what you mean that "row and col values in the data were swapped" Are you using version 1.1.52.post1? Thanks.

[zglu]

Hi Joshua, Yes, I installed 1.1.52.post1 fresh today. It looks like the data was rotated and doesn't overlay with the image correctly.

[joshua-gould]

Thanks. I can reproduce the error now. The row and column pixel spot coordinates are swapped for Space Ranger output prior to version 2.0. Will fix shortly.

[joshua-gould]

Fixed in latest release. Thanks.

[zglu]

Fantastic. Now works beautifully. Thanks again for your prompt support, much appreciated! Have a pleasant weekend :)