Re: metadata and time depiction

Posted by fabrice senger-2 on
URL: http://imagej.273.s1.nabble.com/metadata-and-time-depiction-tp3687079p3687083.html

Hi there,

I hope it's not to boring, I'm still working on file metadata (stk and nd
folders as ganerated by Metamorph).
This time i open my files with the LOCI plugin and ask for the metadata
depicted in the result table...In my case I would have been happy to get the
Results table and not the "Original Metada - filename"...with the Results
table I would have been able to extract whatever info to a custom table.

So i tried to rename the Original-Metadta- table to Results, but this
doesn't work in my hands...

Any clue ?

Thank you very much,

Fabrice.


2010/8/27 Vinay Singh <[hidden email]>

> Hi all,
> I use Metamorph too and have data sets up to 20gb and find it
> Difficult to find time stamps specially after making a maximum projection
> of the z stacks. Would love to know how you are using loci plugin to get the
> time stamp! I am not familiar with programing but I do have the loci plugin
> installed would love a fix I could apply without having to write codes
> Thanks
> Vinay
>
> Vinay Singh
> 4315 FFSC, Duke university
> Durham NC 27708
> 919-6134456
>
> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
> wrote:
>
> > Hello,
> >
> > I had such a piece of discussion off-list with Dan White.
> > As I work with stk files, i have access to the image creation time (this
> is
> > accurate even you pause the acquisition), I have access to this info with
> > the LOCI plugin and some code Melissa kindly sent me.
> >
> > What would be of interest is a tool like a time slider as you can get it
> in
> > Metamorph or in Imaris...or then : "
> >
> >> Are you suggesting that you would like to see the timestamp in seconds
> >> displayed as part of the label at the top of the image window?"
> >>
> >
> >
> >
> > This is probably a particular situation when you have to pause
> acquisition
> > for one or two acquisitions but in this case dynamic measurements would
> not
> > be accurate if based on time intervals (?!)
> >
> > Thank you for your reply,
> >
> > Best,
> >
> > Fabrice.
> >
> > 2010/8/26 Curtis Rueden <[hidden email]>
> >
> >> Hi Fabrice,
> >>
> >> as follow up to a previous mail, i just wonder why the time dimension is
> >>> always depicted as t (time frame) and not in real units as sec.
> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >>> almost every format.
> >>>
> >>
> >> The Bio-Formats Importer does populate the frame interval in the image
> >> properties when that information is available. In the case of variable
> time
> >> between frames, we average the times and populate the frame interval
> with
> >> the mean (though the eventual goal is for ImageJ to support variable
> time
> >> frames directly). And I believe that in general, ImageJ uses the frame
> >> interval value for the frames per second when animating—adjustable by
> right
> >> clicking the Play button next to the time slider.
> >>
> >> Thus it would be interesting to have direct acces to those parameters.
> >>>
> >>
> >> Are you suggesting that you would like to see the timestamp in seconds
> >> displayed as part of the label at the top of the image window?
> >>
> >
> > Yes this is what I think about!
> >
> >>
> >> As example, if you do time-lapse and have to pause your acquisition for
> one
> >>> or two acquisition, you could not use the time interval, but the
> metadata
> >>> acqusitionTime is still relevant.
> >>>
> >>
> >> Whether such a pause is properly recorded in the metadata depends on the
> >> file format. As I said above, Bio-Formats averages the timestamps, so
> you
> >> should still get a reasonable frame interval in the properties, as long
> as
> >> the correct values are really present in metadata.
> >>
> >> -Curtis
> >>
> >> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
> [hidden email]
> >>> wrote:
> >>
> >>> as follow up to a previous mail, i just wonder why the time dimension
> is
> >>> always depicted as t (time frame) and not in real units as sec.
> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >>> almost every format.
> >>>
> >>> Thus it would be interesting to have direct acces to those parameters.
> >>>
> >>> As example, if you do time-lapse and have to pause your acquisition for
> >> one
> >>> or two acquisition, you could not use the time interval, but the
> metadata
> >>> acqusitionTime is still relevant.
> >>>
> >>> Thank you,
> >>>
> >>> Fabrice.
> >>>
> >>
>