Seurat V5 on MERFISH data #7170
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YidaZhang0628
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I have the same question. It seems output from Vizgen MERSCOPE experiments will no longer provide a cell_boundaries folder with .hdf5 files. Instead, the output will include a "cell_boundaries.parquet" file. Are there any plans to update the LoadVizgen() function for use with a parquet file? |
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It seems that you have Cellpose output. I submitted a PR handle Cellpose output #7190 |
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I am planning to use Seurat V5 on a MERFISH dataset. The tutorial uses
LoadVizgen
function to read the files. However, I don't have hdf5r files from segmentation. Therefore, I won't be able to useLoadVizgen
. I can read the data usingReadVizgen
but it results in a plain list instead of a Seurat object. Any idea on how to read MERFISH data without segmentation information into a Seurat object?Beta Was this translation helpful? Give feedback.
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