Reproducing `segmentation_free_allen_smfish` notebook

kharchenkolab / BaysorAnalysis

Analysis for the Baysor paper

MIT License

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Reproducing `segmentation_free_allen_smfish` notebook #2

Open hiraksarkar opened 2 years ago

hiraksarkar commented 2 years ago

Hi,

To run on the data, https://github.com/kharchenkolab/BaysorAnalysis/tree/master/data, do you have instructions on how to run baysor on these samples? I am unable to reproduce the figures from https://github.com/kharchenkolab/BaysorAnalysis/blob/master/notebooks/segmentation_free/segmentation_free_allen_smfish.ipynb

Thanks!

hiraksarkar commented 2 years ago

This pull request https://github.com/kharchenkolab/BaysorAnalysis/pull/3 should create a small tutorial for this.

hiraksarkar commented 2 years ago

Hi @VPetukhov ,

Is it possible to obtain the source or instruction to obtain the dapi_merged.tiff used here /home/vpetukhov/data/spatal/SpaceJam2Full/allen_sm_fish/dapi_merged.tiff