[ome-devel] ScanR importer bit representation

[Rubén Muñoz]

> Hi Ruben,
> 

Hi Melissa
> 
> This is expected; your original ScanR data has 16 bits per pixel, but
> Bio-Formats can only write JPEGs with 8 bits per pixel.

That's very fine because we do not want to loose quality during the conversion.
> 
> Exporting signed data to PNG should work if you update to the latest
> trunk build.  The pixel data is converted from signed to unsigned
> (since PNG does not support signed pixel types), so the pixel type of
> the converted PNG will be 'uint16'.

Tried this, the results was very satisfactory. :)

I have one more concern about bioformats, which is again ScanR specific.

It is great that the importer currently supports different not labelled layouts:

if (wellRows * wellColumns == 0) {
      if (wellLabels.size() <= 96) {
        wellColumns = 12;
      }
      else if (wellLabels.size() <= 384) {
        wellColumns = 24;
      }
      wellRows = wellLabels.size() / wellColumns;
      if (wellRows * wellColumns < wellLabels.size()) wellRows++;
}

There's in fact a third layout (LabTek) which is 12 rows and 32 columns. At the moment this layout is importing because the wells are labeled: A1 to L32

You may notice that the naming convention is the opposite for this layout. Below is the current ScanR naming convention:

store.setPlateRowNamingConvention("A", 0);
store.setPlateColumnNamingConvention("1", 0);

 - Would it possible to detect the LabTek layout and apply a different naming convention? A I said, it has different number of columns and rows than the normal 384 Plates.
 - In addition would it be possible to give the Spot number (1 - 384) to the well name for that particular layout? (something like store.setImageName(new String(i), i);)

I think that these are minor changes but I could upload corresponding datasets (from LabTeks) under request. By now I attach an experiment_descriptor.xml for one of this 384 LabTeks.




Sincerely grateful.

Merry christmas!

Rubén

> 
> Regards,
> -Melissa

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