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Slow opening of SPCImage Data

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.

Slow opening of SPCImage Data

Postby Romain » Thu Mar 13, 2014 1:43 pm

Dear,
I regularly use Bio-format with Fiji for opening and analysing SPCImage Data file (.sdt extension).
However, at the release of the version 5 of Bio-format, I realised that the time taken to open these files was significantly increased (almost 10x longer), using the importer or the macro extension.

I use a PC with windows 8.1 (but tested on Windows 7 also with similar results)
Latest Java (7.51)
ImageJ 1.48s

File description:
256 x 256 x 256 (XYT) .sdt file.

Using Bio-format 5.0.0: it takes about 14 seconds
Using Bio-format 4.4.9 (life line version with ImageJ only update): it takes about 2 seconds

I use batch processing on a regular basis and this time increase is significantly detrimental to my analysis procedure. Has anyone else noticed this slowing down?
Is there a way around it? (not reading the metadata for example)

Thanks a lot for all the help the community brings !!
Regards,

Romain
Romain
 
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Re: Slow opening of SPCImage Data

Postby mlinkert » Sun Mar 23, 2014 11:46 pm

This was also posted on the ome-users mailing list, but we are testing a fix for this issue now:

https://github.com/openmicroscopy/bioformats/pull/984

That fix is expected to be in the upcoming 5.0.1 release of Bio-Formats.
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mlinkert
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