Usage with COSMX data.

[joaolsf]

Hi, this tool seems to have lots of potential but I gotta say the tutorials for usage with different ST is quite lacking!!! Which scripts are for iSCALE-img and which for iSCALE-seq?? The lack of such fundamental information is disappointing…
For example, for fov-based data such as COSMX, there is not really anything much useful in the tutorials in terms of preparing the input data...

Thanks!

[joaolsf]

Ok...I could figure it out myself and run the pipeline in cosmx data. Still, I had to do some editing in the scripts and can't still grasp how different the approach should be for sub-cellular resolution data, as most of the main tutorials/scripts seem to be around spot-based data.

Also, how do you envision the outputs could be integrated in regular spatial omics analysis? For example, how the outputs can be structured in a new cell x gene matrix to continue spatial analysis downstream the whole tissue prediction?