MetaXpress image metadata, and file formats

[Mario Emmenlauer]

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Dear Imaging List,

this is my first post to this list, if it is off-topic or has been
answered before please redirect me to the appropriate place! Thanks.


I have a strange problem with MetaXpress image metadata. When I save
images in the file format "MetaSeries Single-/Multi-Page TIFF", then
Bio-Formats can read a lot more metadata (exposure time, stage coords,
etc) then when saving as "MetaMorph TIFF" file format.

I save images in MetaXpress from a Journal, using "Sequential File Names".
But the Journal setup doesn't allow me to choose the "MetaSeries" file
format, it falls back to "MetaMorph TIFF" wheneber I click "ok"! Is that
a bug? We have a quite recent version (3.1.0.73).


I found a workaround, by editing the Journal with a text editor. When
I replace in Variable "uniqueSetupJNL.stImageType" the "4 .tif" with
"5 .tiff", then MetaXpress will save as "MetaSeries Single-/Multi-Page
TIFF" file format, and all metadata is there!

This is an ugly hack, do you have a better solution to achieve this?
Am I doing something wrong? I'm really new to high content screening
and MetaXpress :-/


All the best,

    Mario

[Tao Tong]

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I mostly use MetaMorph, and also find the metadata from MetaMorph TIFF can
hardly be read by any other software packages.

However, I find the "legacy" stk files are more easily read (metadata-wise)
by all other software packages. So I changed the save preference to use
legacy stk format as default.

In MetaMorph journal front, I usually write a journal to loop through all
images in a folder, change the extension from tif to stk is sufficient to
force MetaMorph to re-save tif into stk format. I don't have MetaXpress, but
I suppose the journal can work in a similar fashion.

Best,

Tao

On Thu, Nov 18, 2010 at 4:54 AM, Mario Emmenlauer <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Imaging List,
>
> this is my first post to this list, if it is off-topic or has been
> answered before please redirect me to the appropriate place! Thanks.
>
>
> I have a strange problem with MetaXpress image metadata. When I save
> images in the file format "MetaSeries Single-/Multi-Page TIFF", then
> Bio-Formats can read a lot more metadata (exposure time, stage coords,
> etc) then when saving as "MetaMorph TIFF" file format.
>
> I save images in MetaXpress from a Journal, using "Sequential File Names".
> But the Journal setup doesn't allow me to choose the "MetaSeries" file
> format, it falls back to "MetaMorph TIFF" wheneber I click "ok"! Is that
> a bug? We have a quite recent version (3.1.0.73).
>
>
> I found a workaround, by editing the Journal with a text editor. When
> I replace in Variable "uniqueSetupJNL.stImageType" the "4 .tif" with
> "5 .tiff", then MetaXpress will save as "MetaSeries Single-/Multi-Page
> TIFF" file format, and all metadata is there!
>
> This is an ugly hack, do you have a better solution to achieve this?
> Am I doing something wrong? I'm really new to high content screening
> and MetaXpress :-/
>
>
> All the best,
>
>    Mario
>

--
http://tongtao.com

[Mario Emmenlauer]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Tao and List,

thanks for the hint with STK, that is nice option too! STK is already
much better than MetaMorph TIFF. However, with careful analysis I found
that the amount of Metadata in the file formats is:
  MetaMorph TIFF  <  MetaMorph STK  <  MetaSeries TIFF

So, there are some attributes in "MetaSeries" format, that are lacking
in both other formats.

Luckily, MolDev support found an answer (though it took quite long, I
didn't even expect it anymore):

> It looks like there is a bug in the dialog.  When you choose MetaMorph
> TIFF or MetaSeries Single\Multi-plane TIFF   it uses whatever is set in
> the Preferences dialog.  Open the Preferences dialog (Edit menu, choose
> the Save tab, check or un-check the “Save Images Using Legacy Format”.

That works for me on MetaXpress 3.1.0.79. The dialog will still show
"MetaMorph TIFF", but will save as "MetaSeries TIFF", so all the Metadata
is there (and readable from LOCI Bio-Formats).

Hope this helps somebody sometime, all the best,

    Mario

> I mostly use MetaMorph, and also find the metadata from MetaMorph TIFF can
> hardly be read by any other software packages.
>
> However, I find the "legacy" stk files are more easily read
> (metadata-wise)
> by all other software packages. So I changed the save preference to use
> legacy stk format as default.
>
> In MetaMorph journal front, I usually write a journal to loop through all
> images in a folder, change the extension from tif to stk is sufficient to
> force MetaMorph to re-save tif into stk format. I don't have MetaXpress,
> but
> I suppose the journal can work in a similar fashion.
>
> Best,
>
> Tao
>
> On Thu, Nov 18, 2010 at 4:54 AM, Mario Emmenlauer
> <[hidden email]>wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear Imaging List,
>>
>> this is my first post to this list, if it is off-topic or has been
>> answered before please redirect me to the appropriate place! Thanks.
>>
>>
>> I have a strange problem with MetaXpress image metadata. When I save
>> images in the file format "MetaSeries Single-/Multi-Page TIFF", then
>> Bio-Formats can read a lot more metadata (exposure time, stage coords,
>> etc) then when saving as "MetaMorph TIFF" file format.
>>
>> I save images in MetaXpress from a Journal, using "Sequential File
>> Names".
>> But the Journal setup doesn't allow me to choose the "MetaSeries" file
>> format, it falls back to "MetaMorph TIFF" wheneber I click "ok"! Is that
>> a bug? We have a quite recent version (3.1.0.73).
>>
>>
>> I found a workaround, by editing the Journal with a text editor. When
>> I replace in Variable "uniqueSetupJNL.stImageType" the "4 .tif" with
>> "5 .tiff", then MetaXpress will save as "MetaSeries Single-/Multi-Page
>> TIFF" file format, and all metadata is there!
>>
>> This is an ugly hack, do you have a better solution to achieve this?
>> Am I doing something wrong? I'm really new to high content screening
>> and MetaXpress :-/
>>
>>
>> All the best,
>>
>>    Mario
>>
>
>
>
> --
> http://tongtao.com
>
>