Image metadata

[José María Mateos]

Hi all,

Is there anyway of reading image metadata? I'm developing a tool for
dynamic clustering and one of the things I'm missing is the frame
duration data. It is trivial to obtain how many frames a image has, but
I can't find how to read how long is each frame.

I don't know if that information is discarded upon data reading, or if
there is any particular plugin that can provide that information.

Best,

José María Mateos.

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

[David Gene Morgan]

José,

        There is a way to read meta-data from many file types:

                Image -> Show Info

I have a simple macro that reads the meta-data and dumps it into a text
file that I can then parse later to find things like the info you want.
  I suspect that there is a way for imageJ to do the same, but I haven't
ever needed that functionality and haven't explored it.

On 08/27/2012 06:42 AM, José María Mateos wrote:

> Hi all,
>
> Is there anyway of reading image metadata? I'm developing a tool for
> dynamic clustering and one of the things I'm missing is the frame
> duration data. It is trivial to obtain how many frames a image has, but
> I can't find how to read how long is each frame.
>
> I don't know if that information is discarded upon data reading, or if
> there is any particular plugin that can provide that information.
>
> Best,
>
> José María Mateos.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
                  David Gene Morgan
                   cryoEM Facility
                   320C Simon Hall
            Indiana University Bloomington
                812 856 1457 (office)
                812 856 3221 (EM lab)
             http://bio.indiana.edu/~cryo

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[Bilel Maalej]

Hi all,

>
>> I am working with ImageJ plugin and i have a problem.
>>
> I have a polygon  ROI selection and i want to obtain continious pixel
coordinate (x,y) in this roi.
Thank's for help
bilel

> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
>
> --
>                  David Gene Morgan
>                   cryoEM Facility
>                   320C Simon Hall
>            Indiana University Bloomington
>                812 856 1457 (office)
>                812 856 3221 (EM lab)
>             http://bio.indiana.edu/~cryo
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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[José María Mateos]

On 27/08/2012 16:34, David Gene Morgan wrote:
>
>      There is a way to read meta-data from many file types:
>
>          Image -> Show Info
>
> I have a simple macro that reads the meta-data and dumps it into a text
> file that I can then parse later to find things like the info you want.
>   I suspect that there is a way for imageJ to do the same, but I haven't
> ever needed that functionality and haven't explored it.

Yes, I can access that metadata from ImageJ that way, but the time data
is missing.

Best,

José María Mateos.

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

[ctrueden]

Hi José,

> I can't find how to read how long is each frame.
>
> I don't know if that information is discarded upon data reading, or
> if there is any particular plugin that can provide that information.

ImageJ does not retain per-frame timestamp data. You can, however, read
that information using Bio-Formats. Here is an example macro:


http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/loci-plugins/utils/macros/planeTimings.txt

Regards,
Curtis

On Mon, Aug 27, 2012 at 5:42 AM, José María Mateos <[hidden email]>wrote:

> Hi all,
>
> Is there anyway of reading image metadata? I'm developing a tool for
> dynamic clustering and one of the things I'm missing is the frame duration
> data. It is trivial to obtain how many frames a image has, but I can't find
> how to read how long is each frame.
>
> I don't know if that information is discarded upon data reading, or if
> there is any particular plugin that can provide that information.
>
> Best,
>
> José María Mateos.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[José María Mateos]

On 27/08/2012 18:32, Curtis Rueden wrote:
> ImageJ does not retain per-frame timestamp data. You can, however, read
> that information using Bio-Formats. Here is an example macro:
>
>
> http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/loci-plugins/utils/macros/planeTimings.txt

Tried that, but doesn't work for my images, which are in Analyze format.

Here's part of the output for the macro you sent me:

Creation date: 2010-04-23T13:44:24
Plane deltas (seconds since experiment began):
Complete.

As you can see, the time deltas are not extracted. This is something
that depends on the type of image that is being read every time, so I
understand this is not an easy problem to solve, but I'd be very
interested in contributing in this improvement if there could be any
chance of doing so.

Best,

José María Mateos.

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

[ctrueden]

Hi José,

> Tried that, but doesn't work for my images, which are in Analyze format.

If you would be willing to send an example Analyze file with variable-width
time stamps, we can investigate adding support for that information in
Bio-Formats. You can upload a sample file from Fiji using the "Help >
Upload Sample Image" feature; please let us know if you do, along with the
expected values of the timestamps.

Regards,
Curtis


On Tue, Aug 28, 2012 at 10:41 AM, José María Mateos <[hidden email]>wrote:

> On 27/08/2012 18:32, Curtis Rueden wrote:
>
>> ImageJ does not retain per-frame timestamp data. You can, however, read
>> that information using Bio-Formats. Here is an example macro:
>>
>>
>> http://trac.openmicroscopy.**org.uk/ome/browser/bioformats.**
>> git/components/loci-plugins/**utils/macros/planeTimings.txt<http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/loci-plugins/utils/macros/planeTimings.txt>
>>
>
> Tried that, but doesn't work for my images, which are in Analyze format.
>
> Here's part of the output for the macro you sent me:
>
> Creation date: 2010-04-23T13:44:24
> Plane deltas (seconds since experiment began):
> Complete.
>
> As you can see, the time deltas are not extracted. This is something that
> depends on the type of image that is being read every time, so I understand
> this is not an easy problem to solve, but I'd be very interested in
> contributing in this improvement if there could be any chance of doing so.
>
>
> Best,
>
> José María Mateos.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[José María Mateos]

On 28/08/2012 18:00, Curtis Rueden wrote:
> If you would be willing to send an example Analyze file with variable-width
> time stamps, we can investigate adding support for that information in
> Bio-Formats. You can upload a sample file from Fiji using the "Help >
> Upload Sample Image" feature; please let us know if you do, along with the
> expected values of the timestamps.

Dear Curtis,

Yes, I'll try to send you a sample image so you can see if there is any
chance of obtaining dynamic data. I'll send it to you as soon as I can
anonymize it.

Best,

José María Mateos.

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