We're Hiring!

combining tiff and csv with metadata

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

combining tiff and csv with metadata

Postby Thorondor » Tue Apr 24, 2012 9:05 am

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.
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining tiff and csv with metadata

Postby jmoore » Thu Apr 26, 2012 12:48 pm

Hi Gideon,

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

Cheers,
~Josh
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany

Re: combining tiff and csv with metadata

Postby Thorondor » Thu Apr 26, 2012 1:23 pm

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.
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining tiff and csv with metadata

Postby jmoore » Thu Apr 26, 2012 1:28 pm

Thorondor wrote: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
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany

Re: combining tiff and csv with metadata

Postby Thorondor » Thu Apr 26, 2012 1:46 pm

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?
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining tiff and csv with metadata

Postby mlinkert » Thu Apr 26, 2012 2:15 pm

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
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Re: combining tiff and csv with metadata

Postby Thorondor » Mon Apr 30, 2012 11:39 am

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
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining tiff and csv with metadata

Postby mlinkert » Tue May 01, 2012 10:54 am

Information on sending a plate sent in a private message.

-Melissa
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin


Return to User Discussion [Legacy]

Who is online

Users browsing this forum: No registered users and 1 guest