[ome-users] Show frame timestamps from proprietary format plugin

[Curtis Rueden]

Hi Josh,


> I've got a proprietary format which stores absolute date-timestamps in
> a footer for each frame, and I have written an ImageJ plugin to open
> these files, and post the timestamps as a list in the Show Info
> dialog, however now I want to display the timestamps on the image or
> in a table (user option). I've come across the following macro, which
> extracts timestamps from Bio-Formats:
>
> https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt
>


Perhaps someone knows how they implement this, or where to look in the
> code. Is there any other way to accomplish my goal?


Bio-Formats is able to perform this operation in a format-agnostic way
because it standardizes metadata from the proprietary file format (PFF)
into the standard OME-XML data model. For details, see the section "A brief
overview of metadata" at:
    http://loci.wisc.edu/bio-formats/about

Your question is becoming a frequently asked one; see these messages from
the ImageJ archive:
    https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;e1955de4.1206
    https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;6e754ad5.1206

In short, you can make calls to the makeText macro function within your
plugin to write your timestamps onto the image planes:
    http://rsb.info.nih.gov/ij/developer/macro/functions.html#makeText

If you think your file format reader is of general interest (and from Aaron
Hendrickson's reply, it sounds like it could be), we would be delighted to
include it with Bio-Formats. See the Bio-Formats File Format Reader Guide
for information on how to create a Bio-Formats reader:

https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/doc/reader-guide.txt

You can use GitHub to good effect here, forking the Bio-Formats project
(from https://github.com/openmicroscopy/bioformats) into your own project
space, implementing your reader on a branch there, and then filing a "Pull
Request" to submit your changes back upstream.

Alternately, you could send us your existing ImageJ plugin and we can
convert it to a Bio-Formats file reader as our time allows.

Regards,
Curtis


On Thu, Jul 12, 2012 at 11:06 AM, Josh Doe <josh at joshdoe.com> wrote:

> I've got a proprietary format which stores absolute date-timestamps in
> a footer for each frame, and I have written an ImageJ plugin to open
> these files, and post the timestamps as a list in the Show Info
> dialog, however now I want to display the timestamps on the image or
> in a table (user option). I've come across the following macro, which
> extracts timestamps from Bio-Formats:
>
> https://github.com/openmicroscopy/bioformats/blob/develop/components/loci-plugins/utils/macros/planeTimings.txt
>
> Perhaps someone knows how they implement this, or where to look in the
> code. Is there any other way to accomplish my goal?
>
> Maybe the concept of frame metadata can be implemented in ImageJ,
> which can consist of simple key value pairs, and perhaps even have a
> few standard keys like microseconds since the Unix epoch, comment,
> etc. An integrated or plugin metadata viewer would then update the
> metadata whenever the stack's current frame is changed.
>
> Thanks,
> -Josh
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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