[ome-users] issue and fix for MetaXpress multi-line descriptions

[Roger Leigh]

On 26/03/15 14:07, Mario Emmenlauer wrote:
>
> Dear Bio-Formats developers,
>
> I have a small issue with MetaXpress meta data, and a possible fix.
> When I read the image (link below), there are several global metadata
> entries that are not correct. I followed up where they come from, and
> it turns out that MetaXpress has a free-text box where user can enter
> a 'Description' for their screening experiment. Multi-line entry is
> supported in MetaXpress, which leads to "wrong" interpretation of the
> metadata in Bio-Formats.
>
> Here the example from the image below. For the field 'Description'
> our user had entered in MetaXpress:
>      siRNA transfection of HeLa cells
>      Entry 4h
>      extracellular: red
>      intracellular: red and green
>      DAPI staining (1:1000)
>      [...]
>
> Of this Description, several lines are missing in Bio-Formats. For
> the text that is not missing, I can find fields like:
>      'extracellular'          'red'
>      'intracellular'          'red and green'
>      'DAPI staining (1'       '1000)'
>
> This is not how I think the metadata should be reported :-)
>
>
> The best solution I could think of is a defined vocabulary of keys
> from MetaXpress, to separate them from the free-text entered by the
> user. Attached is a patch that does exactly this, and works well
> for me. The patch should apply smoothly to Bio-Formats 5.0.7 file
> components/formats-gpl/src/loci/formats/in/MetamorphReader.java
>
> For me, the patch achieves a second functionality: there are some
> keys that do not have a colon, in other words they consist only of
> a key and no value (an example is "Acquired from Photometrics"). For
> me it makes sense to store them as both key and value, i.e. to have
> it reported as:
>      'Acquired from Photometrics' = 'Acquired from Photometrics'
>
> This is my personal preference, you can ignore this part of the patch
> if you do not find it useful.
>
> One last thing: I store the free-text in key 'Global Description'.
> I think for you its more common to use the key 'Global Comment'? Feel
> free to change this to your liking.
>
>
> The image I used is here:
>      http://data.marssoft.de/bBZIX-021_wD13_s3_z0_t1_cCy5_u001.tif

Thanks for the patch.

Looking at it, the behaviour seems generally sensible, though I would
probably just set
   Acquired from Photometrics = 1
to avoid the duplication of information.

Since the description contains free-form metadata which we can't
sensibly parse into key-value pairs, one question I have is whether the
free-text is in a single contiguous block or interspersed with
MetaXpress keys.  For example, if it's e.g. a leading contiguous block,
that would mean we could be a bit more intelligent about processing the
remaining lines--once we've found a known key, we could avoid adding all
subsequent lines to the Comment.  Or if it's always after a certain key
like "Exposure:".  In your example:

------------------------------------------------------------------------
Experiment base name:AC20-2-1--TetR-GFPforEntryAssay
Experiment set:AC20-2-1--TetR-GFPforEntryAssay
siRNA transfection of HeLa cells
infection with ACBr165 (TetR-GFP and const. dsRED
Entry 4h
Induction of TetR-GFP for 4 h together with Gentamycin killing of
extracellular bacteria
extracellular: red
intracellular: red and green
DAPI staining (1:1000)
Dy-647-phalloidin (1:100)
Exposure: 25 ms
Binning: 1 x 1
Region: 1392 x 1040, offset at (0, 0)
Acquired from Photometrics
Subtract: Off
Shading: Off
Digitizer: 20 MHz
Gain: Gain 1 (1x)
Camera Shutter: Always Open
Clear Count: 2
Clear Mode: CLEAR PRE SEQUENCE
Frames to Average: 1
Trigger Mode: Normal (TIMED)
Temperature: -29.95
------------------------------------------------------------------------

Which of these fields are custom?  Are "Experiment base name" and
"Experiment set" custom?  Everything from Exposure looks non-custom.

Another thing is how to handle the parsing if it's not in an XML
Description element.  Currently the code is duplicated in
MetamorphReader after "// parse (mangle) TIFF comment".  If the method
in MetamorphHandler was made static, this could be used here as well, to
remove the duplication.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096