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Vizgen / vizgen-postprocessing

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Convert HDF5 to PARQUET #26

Open Byronxy opened 11 months ago

Byronxy commented 11 months ago

Hi Vizgen developer, I have some segmentation data generated by earlier version with HDF5 format, how can I convert this file with HDF5 format to the PARQUET file generated by latest version?

HeesooSong commented 11 months ago

I am looking for the same. Currently, I am working with the vizgen public human oncology datasets, but they contain HDF5 files instead of a parquet file.

Once it's available, I'm planning to run the post-processing function "partition-transcripts" so that the output detected_transcripts file contains entityID. The detected_transcripts file in the public vizgen data only contains coordinates of each transcript, which makes it very difficult to distinguish from which cell or which plane the transcript is expressed.