Elyas Heidari

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

Hey @xu-ziwei, sorry for the late response, and thanks for your detailed issue. could you let me know what parameters you used for data generation? and how many genes exist...

@mossishahi this is the mask-creation step, that is your segmentation is already over and you have the anndata file and the transcripts file with `segger_cell_id` produced. in order to reproduce...

Hello, @erkinacar5 as mentioned above based on your info, the data has been already segmented, that is transcripts are grouped into new `segger_cell_id`s. Your problem is at the mask-creation step,...

Dear @PietroD thanks for reporting the bug. We have put together a generic platform config: https://github.com/EliHei2/segger_dev/blob/generic_config/platform_guides/platform_preparation_guide.ipynb the idea is to have 2 files: 1) transcripts.parqeut file with `x,y,z`, as well...

Thanks for the contribution @senbaikang! I'm reviewing this, this is similar to the idea of `segger.prediction.predict_multigpu`. It looks fine but I have to test it thoroughly. will do soon!

Dear @joaolsf, It's great to hear that you tried segger on cosmx data. We need to get to the buttom of this as we haven't yet tested segger on cosmx...

Thanks @joaolsf! please feel free to get in touch via email [email protected]! looking forward to get this going. Best.

Dear @MIC0001, the online tutorial is deprecated. Could you please re-clone the repo (re-install if you didn't use `-e` in the pip install, if you did, it's fine). and use...

Hi @quail768, thanks for making a deep dive into segger :) seg2explorer currently works on the previous version of file formats which is .csv.gz, I'm gonna update it for parquet...