Posted by
Mark Hiner-2 on
Aug 14, 2014; 4:05pm
URL: http://imagej.273.s1.nabble.com/SCIFIO-Unusable-tp5009195p5009206.html
Hi Oli,
> Is this mine of samples not exploited when testing out SCIFIO?
The ImageJ2 team uses this data for manual testing. And as you mentioned,
the OME team does extensive automated testing with Bio-Formats, which
directly benefits SCIFIO because it uses Bio-Formats for proprietary file
format support. In the future, we will establish comprehensive automated
testing for SCIFIO itself and its integration with other software
components. See
https://github.com/scifio/scifio/issues/85>Thank you for the reply and I will push people to submit their reports as
well.
The bug reports submitted in the past three months have been fantastic, and
kicked off an extremely productive development drive. Our sincere thanks to
the community for their help and patience.
That said, we agree that having SCIFIO enabled by default has proved too
disruptive for most users at this time. As such, we have now switched it
off by default for new installations. We will reenable it by default only
after addressing all pending bug reports and performance issues.
For anyone who does turn SCIFIO on during this interim period, all bug
reports and feedback will continue to be welcome and helpful.
Thanks again for bringing this topic up today.
- Mark
On Thu, Aug 14, 2014 at 9:53 AM, Burri Olivier <
[hidden email]>
wrote:
> Hi Mark,
>
> Thanks for all the feedback and the information, I understand that SCIFIO
> is user-driven but we feel that we are struggling with issues - which
> BioFormats had solved for us - all over again, which makes it frustrating
> and feels like a bit of a step back alas. Regarding that:
>
> > >We have multichannel tiffs, lsm files, czi files, zvi files lifs
> >
> > It would be a great help if you could ensure these are reported on the
> Fiji
> > BugZilla <
>
http://fiji.sc/bugzilla/buglist.cgi?product=Fiji&resolution=---> > &list_id=1044>.
> > There are reports for some of these formats, but I wasn't sure if they
> were
> > already from you or your team - especially as some were Bio-Formats
> problems
> > (and it sounds like your issues are not).
>
> We did not submit reports at this point, as using BioFormats solves all
> these problems. But from my understanding, does Bioformats not have a
> somewhat extensive database of files of varying formats and flavors that
> they used and that are reported to work with the library. Is this mine of
> samples not exploited when testing out SCIFIO? Thus is by no means a
> reproach, and I apologise if it sounds like one, but I just want to
> understand where these new old problems are creeping up.
>
> Clearly, I need to find the time to submit the if this helps you. Again I
> just don't want to duplicate informations and submissions if you have
> similar data formats already from the years Bioformats has been around.
>
> Also these formats I mentioned are by far some of the most common
> microscopy formats, I do not know what the files I will upload will provide
> that you do not already have.
>
> > You can also point people to the bug reporting section
> > <
http://imagej.net/Bug_reporting_best_practices> of the wiki, which
> > links to "Report a Bug" use and suggests disabling SCIFIO.
> >
> > Thanks for the feedback!
>
> Thank you for the reply and I will push people to submit their reports as
> well.
>
> All the best
>
> Oli
>
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