Re: Problem with calibration info (EXIF data) when opening files

Posted by Mark Hiner-2 on Jun 10, 2014; 1:01pm
URL: http://imagej.273.s1.nabble.com/Problem-with-calibration-info-EXIF-data-when-opening-files-tp5008025p5008112.html

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/45c1f0e6cc68492a3604c93bfbc1
>> >> >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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