Re: metadata and time depiction

Posted by fabrice senger-2 on
URL: http://imagej.273.s1.nabble.com/metadata-and-time-depiction-tp3687079p3687087.html

Hello,

and thank you for the reply.
I use the latest build 1.44G3 (daily build)...
I do not have any problem to access the metadata, with the LOCI plugin
(really great) I can access all the data from my Metamorph files (as I deal
with those) BUT, I couldn't manage to manipulate those datas...This is all
about time-lapse experiments and the ability to use the time data generated
by Metamorph...more over I worked a lot with G. Carpentiers TabStatCustom
Results : you can manipulate the Results table and generate a new custom
table but now, from LOCI I get a table called "Original Metadata -
"filename"", and it is stated I should be able to save this table and
re-open it as a regular Results Table, and I can not manage to do so...

To get around this I can of course export the whole stuff to excel ...

2010/8/31 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>

> On Aug 30, 2010, at 5:06 AM, fabrice senger wrote:
>
> > In addition to this mail : when I try to acces creation date a message
> > appears in the IJ bar :
> >
> > "unknown creation date format : 20100722 14:53:38.88"
> >
> > and when I import my image with metadata in a result window, save that
> table
> > and then reopen it using import results, the table wich opens is still
> not a
> > Results table...and I can not access it (?!)
>
> You can get all the metadata, as a string, of images imported with the
> Bio-Formats plugin using the getMetadata("info") macro function. In the
> ImageJ 1.44g daily build, you can retrieve specified metadata values using
> the getInfo() macro function. For example:
>
>   order = getInfo("DimensionOrder");
>   type = getInfo("PixelType");
>   sizeC = getInfo("SizeC");
>
> The getInfo() function can also retrieve the value of DICOM tags
>
>   modality = getInfo("0008,0060");
>   sliceThickness = getInfo("0018,0050");
>   position = getInfo("0020,0032");
>
> and Java properties
>
>   version = getInfo("java.version");
>   os = getInfo("os.name");
>   home = getInfo("user.home");
>
> -wayne
>
>
> >> 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.
> >>>>>>
> >>>>>
> >>>
> >>
> >>
>