dgault
commented
2 years ago Hi @saramcardle, thank you for opening the Issue and reporting this problem along with the imagesc thread. The CZI reader in Bio-Formats specifically looks for multi filesets to follow a specific naming convention (outlined below), which unfortunately happens to match exactly the same pattern as the appendix which Windows has added. In this scenario it may be possible for the Bio-Formats reader to add some additional sanity checks for the filesets.
// check if we have the master file in a multi-file dataset
// file names are not stored in the files; we have to rely on a
// specific naming convention:
//
// master_file.czi
// master_file (1).czi
// master_file (2).czi
// ...
//
// the number of files is also not stored, so we have to manually check
// for all files with a matching name 
imagesc-bot
melissalinkert
If there are two individual images files in a folder with names like 'X.czi' and 'X (1).czi' bioformats can incorrectly read them as part of a single multi-file dataset. Windows often adds the (1) appendix when a user tries to copy a file into a folder that already contains a file of that name. Then, only the the data/metadata from X.czi will be read, even if X (1).czi is requested.
See here for more information: https://forum.image.sc/t/matlab-bfgetreader-error-with-parentheses-in-file-name/70210
There should be a more robust way of checking whether a file is a part of a multi-file dataset that is less reliant on naming convention.