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glencoesoftware / bioformats2raw

Bio-Formats image file format to raw format converter
GNU General Public License v2.0
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use`--dimension-order`to overwrite one of Z/C/T axis to `position`? #195

Closed BioinfoTongLI closed 1 year ago

BioinfoTongLI commented 1 year ago

Hello there, Many thanks for the great tools! really enjoy using it and it's been a irreplacable tool in our pipeline now.

I am recently having some issue of one microscope producing wrong metadata: tile position saved as T. And the conversion works totally fine. Just with wrong diemnsion information. after reading the help message. It doesn't seem me that there's a possibility to overwirte T to position, i.e. XYZCP using --dimension-order. I am fully aware that this is kind of an edge case, but just wondering if you have any walk-around for this? Best,

melissalinkert commented 1 year ago

@BioinfoTongLI : no, bioformats2raw doesn't have a way to override dimension metadata that comes from Bio-Formats. The --dimension-order option specifies the order in which data should be written, but won't affect how the data is read from the original file(s) (and can't be used to change the number of positions).

If you can share an example dataset that shows this behavior, we can take a look on the Bio-Formats side and see if there are any obvious solutions.

BioinfoTongLI commented 1 year ago

Hi @melissalinkert, that would be great! I can share a google drive link with you. Should I email that link to you instead of posting it here? There will be a master ome.tif and the metadat.txt inside. Both from micro-manager 2.0. They both should be valid. I was converting this stack using bioformats2raw [path-to-master-tif] output.zarr

melissalinkert commented 1 year ago

Should I email that link to you instead of posting it here?

If you don't want to post a public link, best would be to send a private message to https://forum.image.sc/g/ome - that will reach the OME team, which includes everyone who works on Bio-Formats (and me).

BioinfoTongLI commented 1 year ago

@melissalinkert message sent! lmk if you need the rest of tiffs. The one in the folder is just the master. Many thanks!

melissalinkert commented 1 year ago

@BioinfoTongLI : yes, please do upload the complete dataset when you can (I know it's large). It will be difficult for us to test without all of the files.

BioinfoTongLI commented 1 year ago

@melissalinkert all uploaded now!

melissalinkert commented 1 year ago

Thanks for sending the dataset, @BioinfoTongLI. Closing this issue in favor of https://github.com/ome/bioformats/issues/3972.