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Bug 768 - SCIFIO not opening .tif files properly
SCIFIO not opening .tif files properly
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-10 07:50 CDT by Graeme Ball
Modified: 2014-06-10 16:28 CDT
3 users (show)

See Also:
Description Graeme Ball 2014-06-10 07:50:28 CDT 
SCIFIO does not seem to reliably open .tif files (created by ImageJ): where/how should I upload them? In one case, an image '080514CENPNctl-01_R3D_REG.tif' with 305 frames opens as a virtual stack with only 1 frame (virtual stack is not a good default for anything other than massive files). In another case 'Flybrain_3ch_57z_2t.tif', an image with 3 channels, 57Z and 2 frames does not open at all (just gives "Computing min/max complete" in status bar and then ... nothing). 

Has SCIFIO been thoroughly tested on all the bio-formats test data? If not, it may be better to stick with bio-formats as the default for Fiji I/O for now. I guess some people might not understand what is going on if they suddenly can't open some of their images.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.3
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140608215836)
Fiji: http://fiji.sc/update/ (last check:20140608023306)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140604070506)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140519192603)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131220231857)

Files not up-to-date:
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Comment 1 Mark Hiner 2014-06-10 09:04:50 CDT 
Hi Graeme,

>Has SCIFIO been thoroughly tested on all the bio-formats test data? If not, it 
>may be better to stick with bio-formats as the default for Fiji I/O for now.

So I wanted to point out that there is a difference between SCIFIO (https://github.com/scifio/scifio) and what we call SCIFIO that is used by the Fiji I/O (which is really ImageJ2, using SCIFIO for its image I/O). There are many layers here, including an ImageJ 1.x compatibility layer (https://github.com/imagej/imagej-legacy) - which means there are many points for potential failure.

SCIFIO is not fully tested against the Bio-Formats test repository, although it is something we have wanted to do for some time (https://github.com/scifio/scifio/issues/85). But even if all the formats worked perfectly, there would still be problems in the other layers that need to be resolved.

There is a fundamental challenge for small, open-source development teams: we would love to develop our software until it is perfect, to avoid any pain on the user side. But for software of the scope of ImageJ2, it is not reasonable to try and achieve complete test coverage ahead of time.

>I guess some people might not understand what is going on if they suddenly 
>can't open some of their images.

We agree completely. That was exactly why we created a toggle for disabling SCIFIO, so if users needed to get back to classic ImageJ 1.x behavior they could. This was supposed to be well-explained by the "Welcome to ImageJ2" message, but due to problems with it displaying, the ImageJ2 release ended up being more disruptive than we intended.

On the other hand, the ImageJ2 release was pretty much the greatest thing ever for ImageJ2 and SCIFIO development. It has been kicked into high gear, and we've been able to focus on fundamental problems by receiving excellent feedback from users like you.

Our biggest problem right now, I think, is that we're not doing a satisfactory job getting our releases deployed as soon as possible. With a bit of work on our release framework, this should be greatly improved. For example, I think some of these problems you mentioned in this bug report may already be resolved - at the least, error reporting should be improved with the next Fiji update (so you don't just get.. nothing). And Johannes revised the memory detection heuristics (https://github.com/scifio/scifio/commit/5b0c5cf894ad7b458454464215d2556c219b3e67) to mitigate the unnecessary virtual stack creation.

Finally, I wanted it to be clear that ImageJ2 and SCIFIO provide a complete framework for image I/O (among other things). They are highly extensible, and in fact Bio-Formats is already shipped as a plugin for SCIFIO (https://github.com/scifio/scifio-bf-compat) - so when you are using File > Open it's automatically checking Bio-Formats. Because of this, we really don't want to take a step backwards and revert to "just" Bio-Formats, especially as it would again slow our development. As long as users can disable SCIFIO if needed, things are going as intended and we'll just keep knocking out bugs as quickly as possible.

So, when you have problematic images, you can upload them from Fiji via Help > Upload Sample Image and let us know in a bug report. If you upload your failing TIFFs I'll make sure they get tested with the latest Fiji code.

And thank you again for taking the time and patience to report issues. It has really been fantastic this past week to see the level of improvements in SCIFIO and ImageJ2, because of the community's support.
Comment 2 Graeme Ball 2014-06-10 10:17:58 CDT 
Hi Mark,

Thanks for the reply, and sorry if I sounded grumpy / unappreciative (bit tired today perhaps). I noticed the "Upload Sample Image" option, but I wasn't sure it is intended for bug-fixing test images and is private. I have uploaded a smaller version of one of the failing .tif hyperstacks, "Flybrain_3ch_4z_2t.tif", which fails in the same way as the first one I reported (well I *think* I have -- didn't see any feedback). I can upload a shorter version of the multi-frame sequence if needed, and if "Upload Sample Images" is private? (it's unpublished data that comes from somebody else) 

I know it's important for ImageJ2 development that things are released and tested in the wild, and I will persevere with the IJ2/SCIFIO import and continue to report any potential bugs. I do appreciate all the hard work that has gone into these projects, and the responsiveness and helpfulness of everyone involved.

Best regards,

Graeme
Comment 3 Mark Hiner 2014-06-10 10:55:16 CDT 
>Thanks for the reply, and sorry if I sounded grumpy / unappreciative (bit tired 
>today perhaps)

No worries! I totally understand that, because of a few missteps on our part (the welcome message, especially) the ImageJ2 transition was bumpy and caused unnecessary confusion. I'm sure there are others who felt frustrated as well, so that's why I wanted to lay out a complete response to your issues, to ensure our reasoning and intentions are transparent.

>I can upload a shorter version of the multi-frame sequence if needed, and if >"Upload Sample Images" is private?

Upload Sample Images goes to a private page on the Fiji wiki. You need to have a wiki account with special authorization to access these images, so it is intended to accommodate unpublished data. If you'd like, you can see a list of accounts with this authorization here: http://fiji.sc/index.php?title=Special:ListUsers&group=incoming

Thanks!
- Mark
Comment 4 Mark Hiner 2014-06-10 14:53:09 CDT 
Hi Graeme,

 Fiji has been updated with a number of fixes as of a few minutes ago. I tested your Flybrain_3ch_4z_2t.tif dataset with the new version, and it's looking good I think!

 Also, the quality of life issues you mentioned (e.g. opening small datasets as a virtual stack, not opening and not displaying a message) should be resolved.

 Could you test this when you get a chance? Just want to be sure there are no other problems with your data when opened via SCIFIO/ImageJ2 before closing this ticket.

Thanks!
- Mark
Comment 5 Graeme Ball 2014-06-10 15:04:30 CDT 
Oops, mid-air collision on a comment I was just about to make -- here it is repeated:

"After a Fiji update just now, the .tif image I reported a problem with now opens. However, the Edit->Options->ImageJ2 menu item seems to have disappeared: that *is* where it was, right? (perhaps I should've read the ImageJ2 message I got with the update more carefully :-\)"
Comment 6 Graeme Ball 2014-06-10 15:05:52 CDT 
PS. Thanks for the fix :-)
Comment 7 Mark Hiner 2014-06-10 15:08:26 CDT 
>However, the Edit->Options->ImageJ2 menu item seems to have disappeared: that >*is* where it was, right? (perhaps I should've read the ImageJ2 message I got >with the update more carefully :-\)

haha.. nope you're right on here. We merged a patch set at the last second to remove invisible plugins from the menu, and the ImageJ2 options plugin is set to be invisible to hide it in ImageJ2.

Expect it to be fixed shortly...
Comment 8 Johannes Schindelin 2014-06-10 16:28:36 CDT 
It is fixed!