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Question about x_min, x_max in MerscopeSample().load_transcripts() #115
I encountered the following error:
AttributeError: 'MerscopeSample' object has no attribute 'x_min'
Full traceback:
File /segger/src/segger/data/io.py:141, in SpatialTranscriptomicsSample.load_transcripts()
...
x_min = x_min or self.x_min
AttributeError: 'MerscopeSample' object has no attribute 'x_min'
Should I set up the metadata (e.g., call set_metadata()) before calling load_transcripts()?
Or is there something missing in the tutorial example?
changed the title [-]x_min, x_max in MerscopeSample().load_transcripts()[/-][+]Question about x_min, x_max in MerscopeSample().load_transcripts()[/+]on Jun 11, 2025
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[-]x_min, x_max in MerscopeSample().load_transcripts()[/-][+]Question about x_min, x_max in MerscopeSample().load_transcripts()[/+]EliHei2 commentedon Jun 26, 2025
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. in the meantime, we suggest you follow this notebook to preprocess the data in a format which is compatible for segger's use: https://github.com/EliHei2/segger_dev/blob/generic_config/platform_guides/platform_preparation_guide.ipynb
pinging @andrewmoorman to follow up on this thread.
simonmfr commentedon Jul 2, 2025
@EliHei2 Thanks for the great tool! Do you suggest using the workaround for now, or is full MERSCOPE/MERFISH support coming soon?