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bug loading vizgen data #673
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I'm experiencing something similar except it's 16 elements rather than 9?
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Hi @mkunst23 and @andrewjkwok , this should've been fixed in #648, installing |
@michalk8 Thanks for pointing us in the right direction - it works correctly now! |
Sorry it seems it isn't entirely working yet. When I read the data in, my obs dataframe gets all NaNs, but if I check my cell_metadata.csv file, it's looks populated with the various cell coordinates etc. to me. The result is that I have no spatial coordinates to plot. A second quick thing is that previous merscope outputs gave the cell coordinates in a set of hdf5 files, but that has since the merscope software update to v232 and onwards becomes a single parquet file instead - does squidpy need this info at all? I can't seem to find anywhere in the squidpy documentation that uses this file and am wondering if that would help the issue of the lack of spatial coordinates. |
hey @andrewjkwok , thanks for reporting this, I'm afraid it's a bit tricky to help out without the data available. Could you share the data download so we can test it out? thanks! |
@giovp Yes very happy to. Is there an email I could share a google drive link to? Many thanks in advance. |
@andrewjkwok any chance you could point us to some public data? for example, some data shared by vizgen? |
@giovp hmm the problem is that the cell metadata file from my MERSCOPE output (running their latest v232 software) doesn't look the same as the ones that are on vizgen's website. So if I go to the squidpy website and follow the tutorial (https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_vizgen.html) for the data download (https://info.vizgen.com/mouse-brain-map?submissionGuid=a66ccb7f-87cf-4c55-83b9-5a2b6c0c12b9), the I've attached a truncated version of my cell metadata file for reference. Vizgen website data: Output from my merscope: |
hi @andrewjkwok I am unfortunately unable to look into this in the next two weeks, thanks for sharing the data, I'll get back to you soon |
Hi - just wanted to quickly check whether there was any progress with this? |
There was an issue with indexing but installing The spatial coordinates are being populated by the |
Description
Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9
Minimal reproducible example
Traceback
Version
'1.2.2'
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