[ome-devel] ScanR importer bit representation

[Rubén Muñoz]

Correction: LabTek is 12 columns and 32 rows, not the opposite.

Sorry

On Dec 16, 2009, at 10:53 AM, Rubén Muñoz wrote:

>> 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.
> 
> 
> <experiment_descriptor.xml>
> 
> Sincerely grateful.
> 
> Merry christmas!
> 
> Rubén
> 
>> 
>> Regards,
>> -Melissa
> 

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