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KeyError: '72' when reading in Nanostring CosMx data #815
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Have you examined the structure of your fov positions file and the file from the FFPE lung dataset? If you compare them you might see that there is a difference between your file and the example file. The lab I am in has been generating CosMx data from our own machine and we have had to alter the structure of our fov position file in order to get it to match the structure required for the sq.read.nanostring() function. Specifically, we had to take the 'FOV' column in the file, duplicate it to create a column named 'fov', and make that column the index column. It appears that Nanostring has been changing the structure of the flat files as they have been updating their software. We did not have this problem when we analyzed pilot data that was generated by Nanostring in late 2023. We did not have the same error you are describing but it would not have been possible for us to upload our data without altering the fov file. I believe the scverse team will have to update the LoadNanostring function soon as more changes are coming to the structure of the files as Nanostring continues to make their updates. Hopefully this helps in some way. |
hi both, thank you for raising this, indeed it's quite hard to keep track of all the changes that various companies implement on their pipeline's output format. The most up to date readers for technologies can be found in https://spatialdata.scverse.org/projects/io/en/latest/ , could you check if you can read the format with those, and if so it would be possibly easier to then use the spatialdata format in squipdy. |
Hi all, I have used a more updated version of Python (3.11, previously was 3.7). I got a similar error again. I do have FOV 72 in both folders. I am not sure why, it does a similar thing with the data from the other slides but with multiple FOVs. Here is the version of the packages:
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hi @josiejenyne it looks like the |
I am receiving the error below when I am loading in Nanostring data. I am following the same format I had used for the Nanostring FFPE Lung dataset used in the tutorial. I have also restructured the path to have the same exact folders and files as the Lung data. I am not sure what is causing the issue. I am using
sq.read.nanostring()
to read in the data. What is causing this issue? When I read in data from slide 2, I am givenKeyError: '110'
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