[ome-users] Re: Metamorph

[Claude Bonnard]

Hi Ilya

I just did a test to make sure:

On Oct 5,  1:35pm, Ilya Goldberg wrote:
> Subject: Re: [ome-users] Re: Metamorph
> Thanks for Claude's comments.
> An obvious question came up as I was taking a look at the code to
> support this:
> Does MetaMorph STK ever store timepoints in a single STK file, or are
> the timepoints always in separate files?

Each timepoint is stored in a separate "whatever_tn.*" file

> even for single-channel, single-z, multi-t images?

As soon as you have several Z, you build a "stack" and the saved file has the
name "whatever_tn.STK" otherwise it is a  tiff file (its "extension" should be
tiff, since Window$ label it as "tif file" and hide the "extension"

If you have multiple wavelengths, you will generate a tiff file or a STK file
(as above) for each wavelength. The name will contain a  human readable label
of the "wavelength" such as "Cube1 Filter3", but the relative wavelength in nm
is in the file and the "Edit Image Information" function of Metamorph will give
you the totality of the information, including a possible x and y positions
which will come from a motorized equipment.

If you record exactly the same experiment once again in the same directory, you
will add usually (user's choice) an increased indice in the name...

Messy, no?

But as far as I'm concerned, I see a directory as an experiment holding
container: the ideal parser would rely mainly (but not only, since the name is
coming from the individual files!) on the content of the descriptor of the
image, and take the whole file collection together. Every image will have at
least a unique timestamp, no matter it comes from a tiff or a STK


Regards,

Claude
>
> -Ilya
>
> On Oct 5, 2005, at 4:14 AM, Claude Bonnard wrote:
>
> > Hello Ilya,
> >
> > Since I use Metamorph I want to give you my observations:
> >
> > - I can confirm that the files generated by the multidimentional
> > acquisition
> > are ending by .STK (uppercase)
> > - Same for the *_t*.STK for the time-lapse stacks
> > -The last "*" before the .STK is  special at least for people delaing
> > with
> > computer:
> > the first timepoint is: mysample_t1.STK
> > the second		mysample_t2.STK
> > ..
> > the 10th is:		mysample_t10.STK
> >
> > but NOT the logical order: 0001.STK --> 9999.STK
> >
> > As far as I'v heard they don't want to change this, making things a
> > bit more
> > complicated for people who would like to trest their data on other
> > soft.
> >
> > With my best regards
> > Claude
> >
> >
> >
> > On Oct 4,  9:30am, Ilya Goldberg wrote:
> >> Subject: [ome-users] Re: Metamorph
> >> Couple questions:
> >> Is the pattern *_t*.STK always used for the time-lapse in MetaMorph
> >> STKs?  I.e. the timepoint value is the second '*', always preceded by
> >> a
> >> '_t', and always ends with '.STK'?
> >> In other words, the FilenamePattern.RegEx (perl regular expression)
> >> would be:
> >> ^(.+)_t(\d+).STK$
> >> with FilenamePattern.BaseName set to '$1' and FilenamePattern.TheT set
> >> to 2
> >> Is STK always upper-case?
> >>
> >> Anybody familiar with STK (MetaMorph) time-lapse images, please chime
> >> in.
> >>
> >> Thanks!
> >> -Ilya
> >>
> >> On Oct 1, 2005, at 2:14 PM, Jason Swedlow wrote:
> >>
> >>> Hi-
> >>>
> >>> All you RSS maniacs probably saw it, but I checked in a time-lapse 3D
> >>> dataset in Metamorph STK format into TestImages.
> >>>
> >>> Enjoy!
> >>>
> >>> Jason
> >>>
> >>> **************************
> >>> MSI/WTB Complex
> >>> The University of Dundee
> >>> Dow Street
> >>> Dundee  DD1 5EH
> >>> United Kingdom
> >>>
> >>> phone (01382) 345819
> >>> Intl phone:  44 1382 345819
> >>> FAX   (01382) 348072
> >>> email: jason at lifesci.dundee.ac.uk
> >>>
> >>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> >>> Open Microscopy Environment: http://openmicroscopy.org
> >>> **************************
> >>>
> >>> _______________________________________________
> >>> ome-nitpick mailing list
> >>> ome-nitpick at lists.openmicroscopy.org.uk
> >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-nitpick
> >>>
> >>
> >> _______________________________________________
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> >> -- End of excerpt from Ilya Goldberg
> >
> >
> >
> > --
> > Claude Bonnard Ph.D.
> > ISREC (Swiss Institute for Experimental Cancer Research)
> > Microscopy, Imaging and Morphology Core Facility [MIM]
> > Lab F216
> > Ch des Boveresses 155
> > CH-1066 Epalinges
> > Switzerland
> > email: claude.bonnard at isrec.unil.ch
> > phone: [41-21]-692-5891
> >   fax: [41-21]-652-6933
> >
>
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>-- End of excerpt from Ilya Goldberg



-- 
Claude Bonnard Ph.D.
ISREC (Swiss Institute for Experimental Cancer Research)
Microscopy, Imaging and Morphology Core Facility [MIM] 
Lab F216
Ch des Boveresses 155
CH-1066 Epalinges
Switzerland
email: claude.bonnard at isrec.unil.ch
phone: [41-21]-692-5891
  fax: [41-21]-652-6933