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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
https://kharchenkolab.github.io/Baysor/
MIT License
152 stars 31 forks source link

clustering transcripts without segmentation #127

Closed araksm closed 3 weeks ago

araksm commented 3 months ago

Dear all,

Is it possible to get the output of 'clustering molecules' step without proceeding to the segmentation and creating polygons?

Thank you, Araks

VPetukhov commented 2 months ago

Dear Araks, It's possible if you run Baysor from Jupyter Notebooks in Julia. My bad, I haven't documented that option at all, as there were no request for that. But if you need it, I can draft a minimalistic notebook. Otherwise, you can set number of iterations to 1, so the segmentation would go stop very early.

araksm commented 2 months ago

Dear Viktor,

Thank you very much for your email! I guess you refer to --config.segmentation.iters, that would be very helpful!

Thank you again and have a nice day!

Best wishes, Araks

On Wed, 24 Jul 2024 at 21:21, Viktor Petukhov @.***> wrote:

Dear Araks, It's possible if you run Baysor from Jupyter Notebooks in Julia. My bad, I haven't documented that option at all, as there were no request for that. But if you need it, I can draft a minimalistic notebook. Otherwise, you can set number of iterations to 1, so the segmentation would go stop very early.

— Reply to this email directly, view it on GitHub https://github.com/kharchenkolab/Baysor/issues/127#issuecomment-2248534972, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADLIIMDWDD4LH7AO3Z2VTHLZN7PBTAVCNFSM6AAAAABKBUGOW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBYGUZTIOJXGI . You are receiving this because you authored the thread.Message ID: @.***>

VPetukhov commented 2 months ago

Yes, that's the one!