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bio-formats timestamps milliseconds streaming

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mingthor

bio-formats timestamps milliseconds streaming

Hello all,

I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?

Thanks,

Ming

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Melissa Linkert-2

Re: bio-formats timestamps milliseconds streaming

Hi Ming,

> I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?

First, please note that the DeltaT value is intended to store the
time stamp in seconds, and the AcquiredDate value is intended to store a
date stamp in "yyyy-MM-ddTHH:mm:ss" format. See:

http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Image_AcquiredDate
http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Plane_DeltaT

An example macro that displays the plane timings is available here:

https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt

Please note that the Bio-Formats plugin must be installed in order for
the macro to run (see http://loci.wisc.edu/bio-formats/imagej).

The timings can also be seen by selecting the "Display OME-XML metadata"
option when opening the file with the Bio-Formats plugin.

Regards,
-Melissa

On Thu, Jun 21, 2012 at 05:20:19PM -0400, Ming Gao wrote:

> Hello all,
>
> I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?
>
> Thanks,
>
> Ming
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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mingthor

Re: bio-formats timestamps milliseconds streaming

Hi Melissa,

I can display the DeltaT and AcquiredDate now using similar macros. I still have several questions.

1. Since the units for DeltaT is float, I assume it is ok that I store higher resolution timings (e.g., 23.312 s) in this field. Is this right?
2. For streaming, eventually I want to see the timings on the image (display the image and the time together in one image) either through overlay or something else. Do you know if anything could help?

Best regards,
-Ming

-----Original Message-----
From: Melissa Linkert [mailto:[hidden email]] On Behalf Of Melissa Linkert
Sent: Monday, June 25, 2012 12:03 PM
To: Ming Gao
Cc: [hidden email]
Subject: Re: bio-formats timestamps milliseconds streaming

Hi Ming,

> I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?

First, please note that the DeltaT value is intended to store the time stamp in seconds, and the AcquiredDate value is intended to store a date stamp in "yyyy-MM-ddTHH:mm:ss" format. See:

http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Image_AcquiredDate
http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Plane_DeltaT

An example macro that displays the plane timings is available here:

https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt

Please note that the Bio-Formats plugin must be installed in order for the macro to run (see http://loci.wisc.edu/bio-formats/imagej).

The timings can also be seen by selecting the "Display OME-XML metadata"
option when opening the file with the Bio-Formats plugin.

Regards,
-Melissa

On Thu, Jun 21, 2012 at 05:20:19PM -0400, Ming Gao wrote:

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

Melissa Linkert-2

Re: bio-formats timestamps milliseconds streaming

Hi Ming,

> I can display the DeltaT and AcquiredDate now using similar macros. I still have several questions.

Fantastic!

> 1. Since the units for DeltaT is float, I assume it is ok that I store higher resolution timings (e.g., 23.312 s) in this field. Is this right?

Yes, that's correct.

> 2. For streaming, eventually I want to see the timings on the image (display the image and the time together in one image) either through overlay or something else. Do you know if anything could help?

It should be possible to do this with the 'makeText(string, x, y)' macro
function, as documented here:

http://rsb.info.nih.gov/ij/developer/macro/functions.html#M

Regards,
-Melissa

On Mon, Jun 25, 2012 at 06:00:11PM +0000, Ming Gao wrote:

> Hi Melissa,
>
> I can display the DeltaT and AcquiredDate now using similar macros. I still have several questions.
>
> 1. Since the units for DeltaT is float, I assume it is ok that I store higher resolution timings (e.g., 23.312 s) in this field. Is this right?
> 2. For streaming, eventually I want to see the timings on the image (display the image and the time together in one image) either through overlay or something else. Do you know if anything could help?
>
> Best regards,
> -Ming
>
> -----Original Message-----
> From: Melissa Linkert [mailto:[hidden email]] On Behalf Of Melissa Linkert
> Sent: Monday, June 25, 2012 12:03 PM
> To: Ming Gao
> Cc: [hidden email]
> Subject: Re: bio-formats timestamps milliseconds streaming
>
> Hi Ming,
>
> > I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?
>
> First, please note that the DeltaT value is intended to store the time stamp in seconds, and the AcquiredDate value is intended to store a date stamp in "yyyy-MM-ddTHH:mm:ss" format. See:
>
> http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Image_AcquiredDate
> http://git.openmicroscopy.org/src/master/components/specification/Documentation/Generated/OME-2011-06/ome_xsd.html#Plane_DeltaT
>
> An example macro that displays the plane timings is available here:
>
> https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt
>
> Please note that the Bio-Formats plugin must be installed in order for the macro to run (see http://loci.wisc.edu/bio-formats/imagej).
>
> The timings can also be seen by selecting the "Display OME-XML metadata"
> option when opening the file with the Bio-Formats plugin.
>
> Regards,
> -Melissa
>
> On Thu, Jun 21, 2012 at 05:20:19PM -0400, Ming Gao wrote:
> > Hello all,
> >
> > I am saving my high resolution time (millisecond) into OME TIFF AcquiredDate and Pixels/Plane/DeltaT. I want to display this timing info when opening the image through ImageJ. Is there any way to do this, a macro or pluging?
> >
> > Thanks,
> >
> > Ming
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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