Problem with calibration info (EXIF data) when opening files

[GeraldT]

Hi,

I just found a strange behavior in my Fiji (ImageJ version 1.49b):

I have tif images calibrated in mm. When I open the images using drag and drop everything is ok and the image size (30 x 40 mm) is shown in mm in the upper left corner.

If I open the same image from the File menu (Open or Open Recent) the image opens without the mm information, it is now 30 x 40 pixels (992x768) the numbers in parenthesis being the actual size in pixels.

This used to work both ways before.

Mvh
Gerald R. Torgersen
IT-seksjonen,
Det odontologiske fakultet / Faculty of Dentistry
Universitetet i Oslo / University of Oslo

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

[GeraldT]

I tried now to install "plain" ImageJ from the NIH page, updated it to the latest version and there it works both ways. So it looks to be a Fiji problem

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Gerald Ruiner Torgersen
>Sent: Thursday, June 05, 2014 1:24 PM
>To: [hidden email]
>Subject: Problem with calibration info (EXIF data) when opening files
>
>Hi,
>
>I just found a strange behavior in my Fiji (ImageJ version 1.49b):
>
>I have tif images calibrated in mm. When I open the images using drag and
>drop everything is ok and the image size (30 x 40 mm) is shown in mm in the
>upper left corner.
>
>If I open the same image from the File menu (Open or Open Recent) the
>image opens without the mm information, it is now 30 x 40 pixels (992x768)
>the numbers in parenthesis being the actual size in pixels.
>
>This used to work both ways before.
>
>Mvh
>Gerald R. Torgersen
>IT-seksjonen,
>Det odontologiske fakultet / Faculty of Dentistry Universitetet i Oslo /
>University of Oslo
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Mark Hiner-2]

Hi Gerald,

 If you are using an up-to-date Fiji, then you have the latest ImageJ2
<http://developer.imagej.net/2014/06/04/imagej-200-release-candidate>
installed. When you started Fiji after updating, it should have displayed a
"Welcome to ImageJ2" message, and given you an option right away to use
SCIFIO or not for typical image opening - please let me know if these
didn't show up!

 Drag and drop is using ImageJ 1.x right now to perform the opening process
(something that will actually change for drag and dropped images in the
next release) and File > Open uses the ImageJ2 framework - thus the
different display. Not having the calibration information in the
ImageJ2-opened dataset was definitely an oversight, so I filed an issue
<https://github.com/imagej/imagej-legacy/issues/33> and hope to resolve it
quickly. This is exactly why we distributed our release candidate, to get
feedback from users and find the details that we missed.

 In the mean time, if you want to get the old behavior again you can run
"Edit > Options > ImageJ2" and toggle the "Use SCIFIO when opening files"
option. When that option is disabled, you can still use ImageJ2/SCIFIO for
opening files via the "File > Import > Image..." command (which offers
broader file format support, and will automatically use Bio-Formats for
proprietary image formats).

Thank you for testing ImageJ2 and providing feedback!
- Mark


On Thu, Jun 5, 2014 at 6:46 AM, Gerald Ruiner Torgersen <
[hidden email]> wrote:

> I tried now to install "plain" ImageJ from the NIH page, updated it to the
> latest version and there it works both ways. So it looks to be a Fiji
> problem
>
> Mvh
> Gerald R. Torgersen
>
>
> >-----Original Message-----
> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> >Gerald Ruiner Torgersen
> >Sent: Thursday, June 05, 2014 1:24 PM
> >To: [hidden email]
> >Subject: Problem with calibration info (EXIF data) when opening files
> >
> >Hi,
> >
> >I just found a strange behavior in my Fiji (ImageJ version 1.49b):
> >
> >I have tif images calibrated in mm. When I open the images using drag and
> >drop everything is ok and the image size (30 x 40 mm) is shown in mm in
> the
> >upper left corner.
> >
> >If I open the same image from the File menu (Open or Open Recent) the
> >image opens without the mm information, it is now 30 x 40 pixels (992x768)
> >the numbers in parenthesis being the actual size in pixels.
> >
> >This used to work both ways before.
> >
> >Mvh
> >Gerald R. Torgersen
> >IT-seksjonen,
> >Det odontologiske fakultet / Faculty of Dentistry Universitetet i Oslo /
> >University of Oslo
> >
> >--
> >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

[GeraldT]

Hi Mark,

thank you for the reply.  I used SCIFIO, so that was the problem.
I hope that the problem will be fixed soon. Thank you for filing the issue

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Mark Hiner
>Sent: Thursday, June 05, 2014 2:04 PM
>To: [hidden email]
>Subject: Re: Problem with calibration info (EXIF data) when opening files
>
>Hi Gerald,
>
> If you are using an up-to-date Fiji, then you have the latest ImageJ2
><http://developer.imagej.net/2014/06/04/imagej-200-release-candidate>
>installed. When you started Fiji after updating, it should have displayed a
>"Welcome to ImageJ2" message, and given you an option right away to use
>SCIFIO or not for typical image opening - please let me know if these didn't
>show up!
>
> Drag and drop is using ImageJ 1.x right now to perform the opening process
>(something that will actually change for drag and dropped images in the next
>release) and File > Open uses the ImageJ2 framework - thus the different
>display. Not having the calibration information in the ImageJ2-opened dataset
>was definitely an oversight, so I filed an issue
><https://github.com/imagej/imagej-legacy/issues/33> and hope to resolve it
>quickly. This is exactly why we distributed our release candidate, to get
>feedback from users and find the details that we missed.
>
> In the mean time, if you want to get the old behavior again you can run "Edit >
>Options > ImageJ2" and toggle the "Use SCIFIO when opening files"
>option. When that option is disabled, you can still use ImageJ2/SCIFIO for
>opening files via the "File > Import > Image..." command (which offers
>broader file format support, and will automatically use Bio-Formats for
>proprietary image formats).
>
>Thank you for testing ImageJ2 and providing feedback!
>- Mark
>
>
>On Thu, Jun 5, 2014 at 6:46 AM, Gerald Ruiner Torgersen <
>[hidden email]> wrote:
>
>> I tried now to install "plain" ImageJ from the NIH page, updated it to
>> the latest version and there it works both ways. So it looks to be a
>> Fiji problem
>>
>> Mvh
>> Gerald R. Torgersen
>>
>>
>> >-----Original Message-----
>> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> >Gerald Ruiner Torgersen
>> >Sent: Thursday, June 05, 2014 1:24 PM
>> >To: [hidden email]
>> >Subject: Problem with calibration info (EXIF data) when opening files
>> >
>> >Hi,
>> >
>> >I just found a strange behavior in my Fiji (ImageJ version 1.49b):
>> >
>> >I have tif images calibrated in mm. When I open the images using drag
>> >and drop everything is ok and the image size (30 x 40 mm) is shown in
>> >mm in
>> the
>> >upper left corner.
>> >
>> >If I open the same image from the File menu (Open or Open Recent) the
>> >image opens without the mm information, it is now 30 x 40 pixels
>> >(992x768) the numbers in parenthesis being the actual size in pixels.
>> >
>> >This used to work both ways before.
>> >
>> >Mvh
>> >Gerald R. Torgersen
>> >IT-seksjonen,
>> >Det odontologiske fakultet / Faculty of Dentistry Universitetet i
>> >Oslo / University of Oslo
>> >
>> >--
>> >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

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

[Mark Hiner-2]

Hi Gerald,

 Just wanted you to know that I fixed the issue and calibration data is now
being populated correctly on our development branches. This fix should take
effect the next time Fiji is updated (which I think will be later this
afternoon).

 Thank you again for pointing this out!

Regards,
Mark



On Thu, Jun 5, 2014 at 7:20 AM, Gerald Ruiner Torgersen <
[hidden email]> wrote:

> Hi Mark,
>
> thank you for the reply.  I used SCIFIO, so that was the problem.
> I hope that the problem will be fixed soon. Thank you for filing the issue
>
> Mvh
> Gerald R. Torgersen
>
>
> >-----Original Message-----
> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> >Mark Hiner
> >Sent: Thursday, June 05, 2014 2:04 PM
> >To: [hidden email]
> >Subject: Re: Problem with calibration info (EXIF data) when opening files
> >
> >Hi Gerald,
> >
> > If you are using an up-to-date Fiji, then you have the latest ImageJ2
> ><http://developer.imagej.net/2014/06/04/imagej-200-release-candidate>
> >installed. When you started Fiji after updating, it should have displayed
> a
> >"Welcome to ImageJ2" message, and given you an option right away to use
> >SCIFIO or not for typical image opening - please let me know if these
> didn't
> >show up!
> >
> > Drag and drop is using ImageJ 1.x right now to perform the opening
> process
> >(something that will actually change for drag and dropped images in the
> next
> >release) and File > Open uses the ImageJ2 framework - thus the different
> >display. Not having the calibration information in the ImageJ2-opened
> dataset
> >was definitely an oversight, so I filed an issue
> ><https://github.com/imagej/imagej-legacy/issues/33> and hope to resolve
> it
> >quickly. This is exactly why we distributed our release candidate, to get
> >feedback from users and find the details that we missed.
> >
> > In the mean time, if you want to get the old behavior again you can run
> "Edit >
> >Options > ImageJ2" and toggle the "Use SCIFIO when opening files"
> >option. When that option is disabled, you can still use ImageJ2/SCIFIO for
> >opening files via the "File > Import > Image..." command (which offers
> >broader file format support, and will automatically use Bio-Formats for
> >proprietary image formats).
> >
> >Thank you for testing ImageJ2 and providing feedback!
> >- Mark
> >
> >
> >On Thu, Jun 5, 2014 at 6:46 AM, Gerald Ruiner Torgersen <
> >[hidden email]> wrote:
> >
> >> I tried now to install "plain" ImageJ from the NIH page, updated it to
> >> the latest version and there it works both ways. So it looks to be a
> >> Fiji problem
> >>
> >> Mvh
> >> Gerald R. Torgersen
> >>
> >>
> >> >-----Original Message-----
> >> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> >> >Gerald Ruiner Torgersen
> >> >Sent: Thursday, June 05, 2014 1:24 PM
> >> >To: [hidden email]
> >> >Subject: Problem with calibration info (EXIF data) when opening files
> >> >
> >> >Hi,
> >> >
> >> >I just found a strange behavior in my Fiji (ImageJ version 1.49b):
> >> >
> >> >I have tif images calibrated in mm. When I open the images using drag
> >> >and drop everything is ok and the image size (30 x 40 mm) is shown in
> >> >mm in
> >> the
> >> >upper left corner.
> >> >
> >> >If I open the same image from the File menu (Open or Open Recent) the
> >> >image opens without the mm information, it is now 30 x 40 pixels
> >> >(992x768) the numbers in parenthesis being the actual size in pixels.
> >> >
> >> >This used to work both ways before.
> >> >
> >> >Mvh
> >> >Gerald R. Torgersen
> >> >IT-seksjonen,
> >> >Det odontologiske fakultet / Faculty of Dentistry Universitetet i
> >> >Oslo / University of Oslo
> >> >
> >> >--
> >> >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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[dscho]

Hi Mark,

On Thu, 5 Jun 2014, Mark Hiner wrote:

>  Just wanted you to know that I fixed the issue and calibration data is
>  now being populated correctly on our development branches. This fix
>  should take effect the next time Fiji is updated (which I think will be
>  later this afternoon).

Fiji was updated. It also contains fixes for lookup tables and drag 'n
drop issues reported yesterday.

Ciao,
Johannes

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

[GeraldT]

Hi,

I have now updated my Fiji, and it says that no more updates are pending. Still I have the problem with the calibration when using SCIFIO mode.

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Johannes Schindelin
>Sent: Thursday, June 05, 2014 7:19 PM
>To: [hidden email]
>Subject: Re: Problem with calibration info (EXIF data) when opening files
>
>Hi Mark,
>
>On Thu, 5 Jun 2014, Mark Hiner wrote:
>
>>  Just wanted you to know that I fixed the issue and calibration data
>> is  now being populated correctly on our development branches. This
>> fix  should take effect the next time Fiji is updated (which I think
>> will be  later this afternoon).
>
>Fiji was updated. It also contains fixes for lookup tables and drag 'n drop issues
>reported yesterday.
>
>Ciao,
>Johannes
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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[dscho]

Hi Gerald,

On Fri, 6 Jun 2014, Gerald Ruiner Torgersen wrote:

> I have now updated my Fiji, and it says that no more updates are
> pending. Still I have the problem with the calibration when using SCIFIO
> mode.

I did not have a chance to test this yet, so may I ask you to please
download the following two files:

http://jenkins.imagej.net/job/ImageJ-legacy/lastSuccessfulBuild/artifact/target/imagej-legacy-0.5.4-SNAPSHOT.jar

http://jenkins.imagej.net/view/SCIFIO/job/SCIFIO/lastSuccessfulBuild/artifact/scifio/target/scifio-0.14.2-SNAPSHOT.jar

drop them into your Fiji.app/jars/ and remove the obsolete versions
(imagej-legacy-0.5.3.jar and scifio-0.14.2.jar) and test?

Thank you!
Johannes

P.S.: I am sorry that we're not quite there yet, but soon tests like
this will be much easier: you will only need to check an update site to
get the latest development versions, then you can test, and after that you
can uncheck the update site to get back to the stable version. But as I
said, we're not quite there yet (too busy fixing bugs such as the one you
reported).

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

[Mark Hiner-2]

Hi Gerald,

Sorry for the confusion - this is the change
<https://github.com/scifio/scifio/commit/45c1f0e6cc68492a3604c93bfbc196be9bb49698>
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


On Fri, Jun 6, 2014 at 9:13 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Gerald,
>
> On Fri, 6 Jun 2014, Gerald Ruiner Torgersen wrote:
>
> > I have now updated my Fiji, and it says that no more updates are
> > pending. Still I have the problem with the calibration when using SCIFIO
> > mode.
>
> I did not have a chance to test this yet, so may I ask you to please
> download the following two files:
>
>
> http://jenkins.imagej.net/job/ImageJ-legacy/lastSuccessfulBuild/artifact/target/imagej-legacy-0.5.4-SNAPSHOT.jar
>
>
> http://jenkins.imagej.net/view/SCIFIO/job/SCIFIO/lastSuccessfulBuild/artifact/scifio/target/scifio-0.14.2-SNAPSHOT.jar
>
> drop them into your Fiji.app/jars/ and remove the obsolete versions
> (imagej-legacy-0.5.3.jar and scifio-0.14.2.jar) and test?
>
> Thank you!
> Johannes
>
> P.S.: I am sorry that we're not quite there yet, but soon tests like
> this will be much easier: you will only need to check an update site to
> get the latest development versions, then you can test, and after that you
> can uncheck the update site to get back to the stable version. But as I
> said, we're not quite there yet (too busy fixing bugs such as the one you
> reported).
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[GeraldT]

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/45c1f0e6cc68492a3604c93bfbc196b
>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

[Mark Hiner-2]

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/45c1f0e6cc68492a3604c93bfbc196b
> >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
>

--
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[GeraldT]

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

--
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[Mark Hiner-2]

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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[Mark Hiner-2]

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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[GeraldT]

Hi Mark,

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.

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

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