combining tiff and csv with metadata

[Thorondor]

did someone tried something like that, e.g. having 96 tiff files representing one plate and combining this data with a csv file representing metadata and then combining this data, using Bio-Formats and ImageJ or some other tool that uses Bio-Formats so the data can be exported as OME-TIFF or OME-XML later on.

[jmoore]

Hi Gideon,

are you asking this again because you'd like to try without OMERO.tables and just Bio-Formats?

Cheers,
~Josh

[Thorondor]

yes, exactly, could I import data using ImageJ and Bio-Formats, I could later export it as OME-TIFF/XML and then easily load it into omero.

[jmoore]

yes, exactly, could I import data using ImageJ and Bio-Formats, I could later export it as OME-TIFF/XML and then easily load it into omero.

What exactly do you mean by "import data"? Import it into and export it from where if not OMERO?

~J

[Thorondor]

well that's what I am not exactly sure about. :-/

Maybe it is feasible to write a command line tool, that handles tiff and csv files and converts them into ome-xml/tiff using bio-formats. Dunno, does this sound weird to you?

[mlinkert]

Maybe it is feasible to write a command line tool, that handles tiff and csv files and converts them into ome-xml/tiff using bio-formats. Dunno, does this sound weird to you?

There is already a command-line utility to convert a dataset to OME-TIFF using Bio-Formats:

http://loci.wisc.edu/bio-formats/command-line-tools

However, that doesn't solve the general problem of the .csv not being linked to the TIFFs, and in all likelihood the fact that the TIFFs are not grouped together into a plate.

If at all possible, it would be best if you could send us one of the datasets that you're working with. It's likely that we can then update Bio-Formats so that it automatically picks up all of the TIFFs, detects that they are all part of a plate, and attaches the .csv. You would then be able to import them directly into OMERO, with no conversion necessary.

If you need a place to which to upload data, please let me know and I will send you our SFTP server information privately.

-Melissa

[Thorondor]

I can upload one plate (about 1.5GB) and one csv file whith including meta data, so let me know where to upload. I will explain the data in more detail to you, most probably by email.

best regards,
Gideon

[mlinkert]

Information on sending a plate sent in a private message.

-Melissa