SCIFIO Unusable
Locked
 
|
Dear all,
As of right now the SCIFIO library is quite unusable with most of our data. We have multichannel tiffs, lsm files, czi files, zvi files lifs and so far the only thing that works is to disable it and use the classic LOCI formats. So far about once a day we get someone coming over telling us they can no longer open their files and what do you know, SCIFIO is enabled by default and people are not aware of it, causing old macros to stop working or just being unable to open files. Though I understand the motivation behind SCIFIO, I find it too rough to force-enable it every time Fiji gets a major update at this stage of its development. Best Oli -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
On Thursday 14 Aug 2014 07:53:26 you wrote:
> As of right now the SCIFIO library is quite unusable with most of our data. > We have multichannel tiffs, lsm files, czi files, zvi files lifs and so far > the only thing that works is to disable it and use the classic LOCI > formats. > So far about once a day we get someone coming over telling us they can no > longer open their files and what do you know, SCIFIO is enabled by default > and people are not aware of it, causing old macros to stop working or just > being unable to open files. Perhaps related. It seems that the current rc of IJ2 does not macro-record the action of the new Edit>Options>ImageJ2 option. Calling the command is recorded, but not if you click or unclick the option. I always get: run("ImageJ2..."); If it did record it like in IJ1, one way round would be to include the selection of not using SCIFIO in the StartupMacros file. That is very useful to transfer all your default settings to another install. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by Olivier Burri
Hi Oli,
>SCIFIO is enabled by default and people are not aware of it It's true, SCIFIO is a beta product and right now it's a step backwards from classic ImageJ functionality. We enabled it by default because SCIFIO development is driven completely by user feedback, and we're trying to the point where it meets the typical user's day-to-day needs as quickly as we can. That said, I agree that the significance of the "Use SCIFIO when opening files" option is not sufficiently conveyed, and it is not clear that users should try disabling SCIFIO when something goes wrong. On the plus side, this has led to an internal re-evaluation of our error handling and reporting system, and we've started discussion on an interactive troubleshooter plugin that could help identify why images fail to open (and suggest disabling SCIFIO, for example) - although it's lower priority than actual bug and performance fixes for SCIFIO right now. As a temporary improvement I will expand the ImageJ2 options dialog to provide more of a warning when SCIFIO is enabled, and explain when SCIFIO should be disabled. >Though I understand the motivation behind SCIFIO, I find it too rough to force-enable it every time Fiji gets a major >update at this stage of its development. This makes me suspect there may be two bugs that are increasing the severity of the SCIFIO failures. I opened these issues to investigate: * SCIFIO should pass control back to ImageJ when it fails <https://github.com/imagej/imagej-legacy/issues/78> * SCIFIO use state shouldn't be toggled after updates <https://github.com/imagej/imagej-legacy/issues/79> >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). >So far about once a day we get someone coming over telling us they can no longer open their files 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! - Mark On Thu, Aug 14, 2014 at 2:53 AM, Burri Olivier <[hidden email]> wrote: > Dear all, > > As of right now the SCIFIO library is quite unusable with most of our > data. We have multichannel tiffs, lsm files, czi files, zvi files lifs and > so far the only thing that works is to disable it and use the classic LOCI > formats. > > So far about once a day we get someone coming over telling us they can no > longer open their files and what do you know, SCIFIO is enabled by default > and people are not aware of it, causing old macros to stop working or just > being unable to open files. > > Though I understand the motivation behind SCIFIO, I find it too rough to > force-enable it every time Fiji gets a major update at this stage of its > development. > > Best > > Oli > > > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by Mark Hiner-2
Dear ImageJ/Fiji-ers
> is a beta product and right now it's a step backwards > from classic ImageJ functionality. We enabled it by default How is it a coherent strategy to enable beta functionality by default, and foist it upon end users? Is there any plan to have a 'stable' branch of ImageJ2, from which ordinary users can update with some degree of certainty that stuff won't break, and a beta branch for those who like to try the new stuff which might break, and a dev branch for the devs and bug testers, where stuff really is half-broken/half-built most of the time? I realise that IJ2 is still in relatively unstable release-candidate times, but it would be nice to know what future plans may be. My single biggest concern about Fiji is that updates break stuff for users far too often. Sometimes the screams of pain and frustration make it to the mailing list, but I suspect that often they disappear, unheard, in the dark corners of imaging labs around the world. I really hope that as ImageJ2 matures, it adopts a conservative approach to updating userland installations - i.e. only sending stuff to the updater once it's pretty well hardened. Michael <http://www.rvc.ac.uk> This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
Hi Michael,
> Is there any plan to have a 'stable' branch of ImageJ2, from which > ordinary users can update with some degree of certainty that stuff > won't break, and a beta branch for those who like to try the new stuff > which might break, and a dev branch for the devs and bug testers, > where stuff really is half-broken/half-built most of the time? Some components of ImageJ2 and Fiji have indeed migrated to such a model. The stable release of Bio-Formats ships with Fiji, with development versions available from the "Bio-Formats" update site. The situation is similar for TrackMate and SCIFIO, which have the TrackMate-dev and SCIFIO-dev update sites, respectively. It seems likely that this trend will continue. Regards, Curtis On Thu, Aug 14, 2014 at 11:48 AM, Doube, Michael <[hidden email]> wrote: > Dear ImageJ/Fiji-ers > > > is a beta product and right now it's a step backwards > > from classic ImageJ functionality. We enabled it by default > > How is it a coherent strategy to enable beta functionality by default, and > foist it upon end users? > > Is there any plan to have a 'stable' branch of ImageJ2, from which > ordinary users can update with some degree of certainty that stuff won't > break, and a beta branch for those who like to try the new stuff which > might break, and a dev branch for the devs and bug testers, where stuff > really is half-broken/half-built most of the time? I realise that IJ2 is > still in relatively unstable release-candidate times, but it would be nice > to know what future plans may be. > > My single biggest concern about Fiji is that updates break stuff for users > far too often. Sometimes the screams of pain and frustration make it to the > mailing list, but I suspect that often they disappear, unheard, in the dark > corners of imaging labs around the world. I really hope that as ImageJ2 > matures, it adopts a conservative approach to updating userland > installations - i.e. only sending stuff to the updater once it's pretty > well hardened. > > Michael > > > > > <http://www.rvc.ac.uk> > > This message, together with any attachments, is intended for the stated > addressee(s) only and may contain privileged or confidential information. > Any views or opinions presented are solely those of the author and do not > necessarily represent those of the Royal Veterinary College. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
I believe that I am having a similar problem to the one that Michael posted. FIJI recently did a big update and now when I try to open images in FIJI there are automatic adjustments made. I usually disable that feature in the bioformats importer. I did some searching and found out about the switch to SCIFO. However, I tried to disable it from being the default and that doesn't seem to be working. Also, I recently got a new computer and did a fresh install of FIJI. For some reason the bioformats plugin is not working either even though it said that installation was successful. I can't get the dialog box to open. All of these problems started happening after the update and it took me a little bit to notice what seemed wrong when opening the images.
Thank you for your help! |
|
|
On 8/15/14, 6:13 PM, Jordan Cocchiaro wrote:
> I believe that I am having a similar problem to the one that Michael posted. > FIJI recently did a big update and now when I try to open images in FIJI > there are automatic adjustments made. I usually disable that feature in the > bioformats importer. I did some searching and found out about the switch to > SCIFO. However, I tried to disable it from being the default and that > doesn't seem to be working. Also, I recently got a new computer and did a > fresh install of FIJI. For some reason the bioformats plugin is not working > either even though it said that installation was successful. I can't get > the dialog box to open. All of these problems started happening after the > update and it took me a little bit to notice what seemed wrong when opening > the images. > > Thank you for your help! > I have the most recent FIji update, with SCIFIO disabled, and I have no problem with bioformats import. Here are some tips: 1. Disable the Bioformats update site. You get bioformats with Fiji, and that version is less likely to have problems. 2. Disable any other update sites if you do not need them. Many problem have been caused by conflicts with some sites, though much of that has been solved. 3. Use the buzilla bug reporter that is built into FIji (Help>Report a Bug). I have had many bug promptly solved through this system. --aryeh -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
Thanks for your message, Aryeh! Jordan L. Cocchiaro, PhD Postdoctoral Fellow Rawls Laboratory Duke University Dept. of Molecular Genetics and Microbiology 213 Research Drive 327 CARL Bldg. DUMC Box 3580 Durham, NC 27710 Lab phone: 919-660-0894 From: Aryeh Weiss [via ImageJ] [mailto:ml-node+[hidden email]]
On 8/15/14, 6:13 PM, Jordan Cocchiaro wrote:
If you reply to this email, your message will be added to the discussion below: http://imagej.1557.x6.nabble.com/SCIFIO-Unusable-tp5009195p5009235.html
To unsubscribe from SCIFIO Unusable,
click here. |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |