Error in cell under Copy one csv containing the channel order of the full stack in to the cellprofiler input folder

[rachel662]

Hi there, I'm having some trouble running a dataset through the ipynb notebook, I get an error in the previous cell where it says keyname and a specific channel, but running the next cell anyway I get this error

StopIteration Traceback (most recent call last)

in ----> 1 fn = next(folder_path_analysis.glob(f'*{suffix_full}.csv')) 2 3 shutil.copy(fn, file_path_full_channels_csv) StopIteration: if anyone would be able to help at all I would really appreciate it thanks so much Rachel

[votti]

Hi Rachel,

Sorry for taking so long: The meaning of the error in the cell above is that according to the metadata your panel.csv, there should be a metal channel in the images that was not actually acquired in your data and is thus missing, causing this error and causing no files being converted. This also causes no f'*{suffix_full}.csv files being generated, which then causes the subsequent cells to fail as well.

Please make sure that only channels actually acquired in your data are present in your panel .csv file.

Cheers, Vito

I will open an issue in Imctools to give a more readable error message in these cases. Best, Vito

[nilseling]

Closing due to inactivity