Tif Stacks Not Opening Correctly

[J. Daniel Fenn]

I'm curious if anyone has run in to this problem.

I have a stack saved as a .tif image (multi-page tif).  The stack has 23
images/pages within the stack.  The stack (all 23 images) open fine on
any imaging program I have access to (Gimp, photoshop, exiv2, etc).

But when I open the stack in Fiji, it only finds 20 of the 23 images.  I
have this same problem on multiple images, but each one is slightly
different.  Some are missing 3 planes, some are missing 1, some are
missing 10 planes.  Again, on all other imaging software all planes show up.

I have no idea where to even begin to troubleshoot this problem.  Does
anyone have any ideas?  I have discovered that the images open fine in
older version of Fiji (the life-line versions).  The older versions I
get all 23 planes as expected.

Am I doing something wrong?

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[ctrueden]

Hi J. Daniel,

> I have discovered that the images open fine in older version of Fiji
> (the life-line versions).  The older versions I get all 23 planes as
> expected.

Please try running Edit > Options > ImageJ2 and disabling the "Use SCIFIO
when opening files" option, then opening your TIFFs again. Do they open
correctly? If so, it is a problem with the new SCIFIO support.

If that is the case, it would be very helpful if you could send a sample
non-working TIFF file using the Help > Upload Sample Image command.

Thanks,
Curtis


On Thu, Jul 10, 2014 at 3:28 PM, J. Daniel Fenn <[hidden email]
> wrote:

> I'm curious if anyone has run in to this problem.
>
> I have a stack saved as a .tif image (multi-page tif).  The stack has 23
> images/pages within the stack.  The stack (all 23 images) open fine on
> any imaging program I have access to (Gimp, photoshop, exiv2, etc).
>
> But when I open the stack in Fiji, it only finds 20 of the 23 images.  I
> have this same problem on multiple images, but each one is slightly
> different.  Some are missing 3 planes, some are missing 1, some are
> missing 10 planes.  Again, on all other imaging software all planes show
> up.
>
> I have no idea where to even begin to troubleshoot this problem.  Does
> anyone have any ideas?  I have discovered that the images open fine in
> older version of Fiji (the life-line versions).  The older versions I
> get all 23 planes as expected.
>
> Am I doing something wrong?
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[J. Daniel Fenn]

Curtis,

It does appear to open correctly when I turn off SCIFIO.  I will upload
a sample stack later today.  Thanks!

-Dan

On 07/10/2014 11:41 PM, Curtis Rueden wrote:

> Hi J. Daniel,
>
> > I have discovered that the images open fine in older version of Fiji
> > (the life-line versions).  The older versions I get all 23 planes as
> > expected.
>
> Please try running Edit > Options > ImageJ2 and disabling the "Use
> SCIFIO when opening files" option, then opening your TIFFs again. Do
> they open correctly? If so, it is a problem with the new SCIFIO support.
>
> If that is the case, it would be very helpful if you could send a
> sample non-working TIFF file using the Help > Upload Sample Image command.
>
> Thanks,
> Curtis
>
>
> On Thu, Jul 10, 2014 at 3:28 PM, J. Daniel Fenn
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     I'm curious if anyone has run in to this problem.
>
>     I have a stack saved as a .tif image (multi-page tif).  The stack
>     has 23
>     images/pages within the stack.  The stack (all 23 images) open fine on
>     any imaging program I have access to (Gimp, photoshop, exiv2, etc).
>
>     But when I open the stack in Fiji, it only finds 20 of the 23
>     images.  I
>     have this same problem on multiple images, but each one is slightly
>     different.  Some are missing 3 planes, some are missing 1, some are
>     missing 10 planes.  Again, on all other imaging software all
>     planes show up.
>
>     I have no idea where to even begin to troubleshoot this problem.  Does
>     anyone have any ideas?  I have discovered that the images open fine in
>     older version of Fiji (the life-line versions).  The older versions I
>     get all 23 planes as expected.
>
>     Am I doing something wrong?
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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[ctrueden]

Hi Dan,

> I will upload a sample stack later today.

Did you get a chance to upload a sample TIFF yet? I don't see any new
recent uploads since your mail.

> But when I open the stack in Fiji, it only finds 20 of the 23 images.

I would really like to investigate this bug, since we have had at least one
other report of "missing image planes" similar to this.

Thanks,
Curtis


On Fri, Jul 11, 2014 at 7:15 AM, J. Daniel Fenn <[hidden email]
> wrote:

>  Curtis,
>
> It does appear to open correctly when I turn off SCIFIO.  I will upload a
> sample stack later today.  Thanks!
>
> -Dan
>
>
> On 07/10/2014 11:41 PM, Curtis Rueden wrote:
>
> Hi J. Daniel,
>
>  > I have discovered that the images open fine in older version of Fiji
> > (the life-line versions).  The older versions I get all 23 planes as
> > expected.
>
>  Please try running Edit > Options > ImageJ2 and disabling the "Use
> SCIFIO when opening files" option, then opening your TIFFs again. Do they
> open correctly? If so, it is a problem with the new SCIFIO support.
>
>  If that is the case, it would be very helpful if you could send a sample
> non-working TIFF file using the Help > Upload Sample Image command.
>
>  Thanks,
> Curtis
>
>
> On Thu, Jul 10, 2014 at 3:28 PM, J. Daniel Fenn <
> [hidden email]> wrote:
>
>> I'm curious if anyone has run in to this problem.
>>
>> I have a stack saved as a .tif image (multi-page tif).  The stack has 23
>> images/pages within the stack.  The stack (all 23 images) open fine on
>> any imaging program I have access to (Gimp, photoshop, exiv2, etc).
>>
>> But when I open the stack in Fiji, it only finds 20 of the 23 images.  I
>> have this same problem on multiple images, but each one is slightly
>> different.  Some are missing 3 planes, some are missing 1, some are
>> missing 10 planes.  Again, on all other imaging software all planes show
>> up.
>>
>> I have no idea where to even begin to troubleshoot this problem.  Does
>> anyone have any ideas?  I have discovered that the images open fine in
>> older version of Fiji (the life-line versions).  The older versions I
>> get all 23 planes as expected.
>>
>> Am I doing something wrong?
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Dan,

> I just uploaded it.  Sorry for the delay.

No worries, we received the file and can reproduce the problem. Both SCIFIO
and Bio-Formats (which have very similar TIFF reading code) only identify
20 planes instead of the full 23. I filed an issue:

https://github.com/scifio/scifio/issues/212

We will investigate and fix when we can.

Regards,
Curtis


On Mon, Jul 14, 2014 at 12:00 PM, J. Daniel Fenn <
[hidden email]> wrote:

>  Hi Curtis,
>
> I just uploaded it.  Sorry for the delay.
>
> I didn't get any sort of confirmation that it uploaded.  The file was
> named 02-4_PE.tif
>
> Let me know if I can help out in any other way.
>
> Best,
> -Dan
>
> If it didn't upload I can maybe try sending it to you directly.  I don't
> know how to tell for sure if it uploaded or not.
>
>
> On 07/14/2014 12:23 PM, Curtis Rueden wrote:
>
> Hi Dan,
>
>  > I will upload a sample stack later today.
>
>  Did you get a chance to upload a sample TIFF yet? I don't see any new
> recent uploads since your mail.
>
>  > But when I open the stack in Fiji, it only finds 20 of the 23 images.
>
>  I would really like to investigate this bug, since we have had at least
> one other report of "missing image planes" similar to this.
>
>  Thanks,
> Curtis
>
>
> On Fri, Jul 11, 2014 at 7:15 AM, J. Daniel Fenn <
> [hidden email]> wrote:
>
>>  Curtis,
>>
>> It does appear to open correctly when I turn off SCIFIO.  I will upload a
>> sample stack later today.  Thanks!
>>
>> -Dan
>>
>>
>> On 07/10/2014 11:41 PM, Curtis Rueden wrote:
>>
>> Hi J. Daniel,
>>
>>  > I have discovered that the images open fine in older version of Fiji
>> > (the life-line versions).  The older versions I get all 23 planes as
>> > expected.
>>
>>  Please try running Edit > Options > ImageJ2 and disabling the "Use
>> SCIFIO when opening files" option, then opening your TIFFs again. Do they
>> open correctly? If so, it is a problem with the new SCIFIO support.
>>
>>  If that is the case, it would be very helpful if you could send a
>> sample non-working TIFF file using the Help > Upload Sample Image command.
>>
>>  Thanks,
>> Curtis
>>
>>
>> On Thu, Jul 10, 2014 at 3:28 PM, J. Daniel Fenn <
>> [hidden email]> wrote:
>>
>>> I'm curious if anyone has run in to this problem.
>>>
>>> I have a stack saved as a .tif image (multi-page tif).  The stack has 23
>>> images/pages within the stack.  The stack (all 23 images) open fine on
>>> any imaging program I have access to (Gimp, photoshop, exiv2, etc).
>>>
>>> But when I open the stack in Fiji, it only finds 20 of the 23 images.  I
>>> have this same problem on multiple images, but each one is slightly
>>> different.  Some are missing 3 planes, some are missing 1, some are
>>> missing 10 planes.  Again, on all other imaging software all planes show
>>> up.
>>>
>>> I have no idea where to even begin to troubleshoot this problem.  Does
>>> anyone have any ideas?  I have discovered that the images open fine in
>>> older version of Fiji (the life-line versions).  The older versions I
>>> get all 23 planes as expected.
>>>
>>> Am I doing something wrong?
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>>
>
>

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