[ome-devel] Re: [ome-users] Re: Metamorph

Thu Oct 6 14:42:12 BST 2005

OK, this makes sense.
Looking at some STKs that I have, there is indeed wavelength 
information stored within the file (in addition to the filename), but 
it appears that its not always valid (sometimes its the emission 
wavelength, sometimes its all zeros).
Basically the importer will be able to handle both cases (multi-wave in 
single STK, or multi-wave in multiple STKs).  It will be able to store 
the human-readable fluor that follows the _wnnnFLUOR pattern, and it 
will look inside the file for a valid emission wavelength.  What it 
wont be able to deal with is a case where there are multiple 
wavelengths specified inside the file, as well as wavelengths specified 
in the filename.  Basically because the filename is limited to a single 
wavelength, and you can't determine which of the wavelengths within the 
file correspond to the wavelength specified in the filename.  I'm not 
sure such a case can even be rescued because there is no basis to 
decide which of the conflicting information is correct.  Hopefully such 
cases don't actually exist.  If wavelengths as well as timepoints are 
always in separate files, and the STK is only used for multiple Zs, 
then this will just work transparently.

Unfortunately, I'm totally tied up right now and can't put any effort 
into this for at least a week.  But at least its clear what's needed 
now, and its not even very difficult.  Basically the logic from the 
multi-file importers (HTD, TIFF, pic, etc) needs to be merged with the 
STK importer.  Its a well established pattern that we've followed 
before, and STK doesn't present any significant deviations from it.

Thanks for your help looking into this.
-Ilya

On Oct 6, 2005, at 8:10 AM, Claude Bonnard wrote:

> 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
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>>>>>
>>>>
>>>> _______________________________________________
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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
>>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>> -- 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
>