Bug 841 – hyperstack not switching between Z positions

Bug 841 - hyperstack not switching between Z positions


Summary:	hyperstack not switching between Z positions

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	ImageJ2
Version:	unspecified
Hardware:	PC Windows

Importance:	P5 major
Assigned To:	ImageJ Developers Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-07-07 15:07 CDT by Joshua Kelley
Modified:	2014-07-14 13:43 CDT
CC List:	1 user (show)

See Also:

Description Joshua Kelley 2014-07-07 15:07:33 CDT

I convert my stack of 870 images to 6 z positions and 145 time points.  The z position does not change when I alter the z-position slider however.  Attempting to do something like a z-projection gives images that flicker in intensity, so I think that it is not just rendering of different z-positions, but also acting upon them that is messed up.  This seemed to be find before I updated today.

Comment 1 Mark Hiner 2014-07-10 15:03:16 CDT

Hi Joshua,

 It's not entirely clear what steps to take to reproduce this issue (e.g. image format of the dataset, whether it was opened with File>Open or via the Bio-Formats importer, etc..).

 Could you take a look at http://fiji.sc/Bug_reporting_best_practices and then update this bug report? Uploading a sample image and pasting the local environment of your ImageJ installation would be especially helpful. That wiki page also has temporary workaround instructions until we can resolve the issue.

Thanks for the report!

Comment 2 Joshua Kelley 2014-07-11 11:38:34 CDT

After updating FIJI today, this bug no longer happens.

Comment 3 Mark Hiner 2014-07-11 11:41:43 CDT

Joshua,

 Can you check your Edit > Options > ImageJ2 settings?

 If "Use SCIFIO when opening files" is unchecked, could you enable it and then see if this bug is still present? I just want to be sure it's not a bug in the ImageJ2 side.

 If the option is checked and you still can't reproduce the error, we can close this issue.

Thanks!

Comment 4 Joshua Kelley 2014-07-14 11:43:11 CDT

I did this, and while SCIFIO doesn't do a good job of opening my images, once images are open, I do not get the hyperstack bug, so I think its safe to close that.

Comment 5 Mark Hiner 2014-07-14 11:52:41 CDT

I am assuming by "doesn't do a good job" you mean that it is slower than you're used to, an issue beyond the scope of this bug report and discussed elsewhere.

If there is actually an issue with correctness in opening your dataset, please re-open this issue or file a new one.

Thanks.

Comment 6 Joshua Kelley 2014-07-14 13:08:55 CDT

What I mean, precisely, is that I cannot do an apples to apples comparison of stack to hyperstack transition, and resultant movement through the hyperstack, because with SCIFIO enabled, I cannot import the same images that I was converting from stack to hyperstack, and then trying to navigate through.  

I am importing 145 16 bit .tif files, each of which has 6 layers.  With SCIFIO enabled, it seems to be picking multiple channels, and opening a subset of the time points it should be, and then it opens one image a couple thousand times.     

This is a problem with SCIFIO importing though, so I assume it is not applicable to this specific bug.  It did appear that I could navigate the z dimension properly after converting to a hyperstack, but SCIFIO opened many of the same images over and over again, so it would formally be possible for me to not see certain types of errors.

Comment 7 Mark Hiner 2014-07-14 13:43:58 CDT

I agree, it is not related to this bug. Another report should be opened for the incorrect importing.

Could be related to https://github.com/imagej/imagej-legacy/issues/61

A sample dataset would be helpful, too.