Elyas Heidari

I think it would be great to have the flexibility to add more columns to the shepes' geopandas dataframes, this is super useful, as sometimes having shapes that are not...

Hey @rusty1s, Thanks for your quick repsonse. Adding `batch_size` indeed solves the problem (see the following code). I overlooked the traceback, was kinda obvious 😅. ``` ... self.log("validation_loss", loss, on_step=False,...

Thanks Luca! Sorry for opening again, there's another error still, which I can guess where's it from (i.e., not reading cell boundaries) but leave it here: ``` line 344, in...

Hi @ccruizm thanks for reporting the issue. We are still experimenting with CosMx, therefore the branch is not stable yet and is subject to many changes in the coming weeks....

@ccruizm sorry for the late response. you could find the notebooks on this branch: https://github.com/EliHei2/segger_dev/tree/generic_config and therefore please install this branch, or switch to this branch once cloned.

Hi @asmariyaz23 I assume you're running the pipeline on 5K panel? In this case the tokenized version runs slowly, we will fix this, but for now it's recommended to use...

Hey @jpark27 thanks for reaching out. you can use the boundary module in segger.validation as the following to generate non-convex cell boundaries, it's the same algorithm impelmented by baysor. ```...

Dear @marzaidi parameter tuning is still under development we are foreseeing solving it in January. Thanks for your patience!

Hey @marzaidi the hyperparam tuning is deprecated and we will update it soon. thanks for reporting this.

please refer to #121