http://imagej.273.s1.nabble.com/Problem-with-calibration-info-EXIF-data-when-opening-files-tp5008025p5008120.html
thank you very much. Now it works perfectly :-)
I really appreciate the effort you and all the other developers are putting in to make this fantastic program for us.
Gerald R. Torgersen
>-----Original Message-----
>From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
>Mark Hiner
>Sent: Tuesday, June 10, 2014 3:01 PM
>To:
[hidden email]
>Subject: Re: Problem with calibration info (EXIF data) when opening files
>
>Hi Gerald,
>
> Indeed this was a bug with the SCIFIO TIFFFormat. We were reading
>calibration units but not actually using them. I opened an issue here:
>
https://github.com/scifio/scifio/issues/195>
> It's already fixed locally, and your data opened with "mm" units for me.
>So this will go live in the next Fiji update.
>
>Thanks again for reporting the issue and providing your sample data.
>- Mark
>
>
>On Tue, Jun 10, 2014 at 7:46 AM, Mark Hiner <
[hidden email]> wrote:
>
>> Great! thanks! I'll test it right now.
>>
>>
>> On Tue, Jun 10, 2014 at 7:44 AM, Gerald Ruiner Torgersen <
>>
[hidden email]> wrote:
>>
>>> Hi Mark,
>>>
>>> I have done that, two different images scaled in different ways, but
>>> booth in mm:
>>> 1000px-Graph-paper.tif - test image calibrated manually using ImageJ
>>> 20131106-134636.0-IO.tif - radiograph, converted from DICOM image,
>>> calibrated by macro using DICOM header information
>>>
>>> Mvh
>>> Gerald R. Torgersen
>>>
>>>
>>> >-----Original Message-----
>>> >From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf
>>> >Of Mark Hiner
>>> >Sent: Tuesday, June 10, 2014 2:24 PM
>>> >To:
[hidden email]
>>> >Subject: Re: Problem with calibration info (EXIF data) when opening
>>> >files
>>> >
>>> >Hi Gerald,
>>> >
>>> > Can you use the "Help > Upload Sample Image" command in Fiji to
>>> >upload your dataset? I need to do more in-depth debugging to see if
>>> >it's a
>>> problem
>>> >with reading the metadata of your image, or in reporting the
>>> >calibration
>>> values.
>>> >
>>> >Thank you!
>>> >- Mark
>>> >
>>> >
>>> >On Tue, Jun 10, 2014 at 1:47 AM, Gerald Ruiner Torgersen <
>>> >
[hidden email]> wrote:
>>> >
>>> >> Hi Mark,
>>> >>
>>> >> thank you for explaining. I have now tried the updated version,
>>> >> and there is still an issue: My images calibrated in mm are now
>>> >> showing up
>>> in µm.
>>> >> The µm are not scaled, but an image 30 x 40 mm is now showing as
>>> >> 30 x
>>> >> 40 µm.
>>> >>
>>> >> When I turn off SCIFIO the are shown with correct unit of length (mm).
>>> >>
>>> >>
>>> >> Mvh
>>> >> Gerald R. Torgersen
>>> >>
>>> >> >-----Original Message-----
>>> >> >From: ImageJ Interest Group [mailto:
[hidden email]] On
>>> >> >Behalf Of Mark Hiner
>>> >> >Sent: Friday, June 06, 2014 5:11 PM
>>> >> >To:
[hidden email]
>>> >> >Subject: Re: Problem with calibration info (EXIF data) when
>>> >> >opening files
>>> >> >
>>> >> >Hi Gerald,
>>> >> >
>>> >> >Sorry for the confusion - this is the change
>>> >> ><
https://github.com/scifio/scifio/commit/45c1f0e6cc68492a3604c93b>>> >> >fbc1
>>> >> >96b
>>> >> >e9bb49698>
>>> >> >fixing calibration in SCIFIO (and there is a corresponding change
>>> >> ><
https://github.com/imagej/imagej->>> >> >legacy/commit/9176fd86289fe83c6efab355ed04674b334d6718>
>>> >> >in imagej-legacy). These changes were complete but un-released as
>>> >> >of last night/this morning. By default, we only update Fiji with
>>> released code.
>>> >> >
>>> >> >Johannes asked you to test with our development code (and thus
>>> >> >the "SNAPSHOT" in the .jar name) but I should have just released
>>> >> >the changes when they were ready and uploaded them to Fiji.
>>> >> >
>>> >> > SCIFIO 0.14.2 and imagej-legacy 0.5.4 are now released and
>>> >> > uploaded to
>>> >> Fiji. If
>>> >> >you update again you should get them. Please let us know if this
>>> >> >doesn't
>>> >> work
>>> >> >or if you still have calibration issues.
>>> >> >
>>> >> >Thanks again,
>>> >> >Mark
>>> >> >
>>> >> >
>>> >>
>>> >>
>>> >> --
>>> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>> >>
>>> >
>>> >--
>>> >ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>
>>
>
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