[ome-devel] ScanR importer bit representation

[Melissa Linkert]

Hi Ruben,

> We are
> concerned that ScanR software is storing signed bit images, but part of the
> code reads:
>
>    reader = new MinimalTiffReader();
>    reader.setId(tiffs[0]);
>    int sizeX = reader.getSizeX();
>    int sizeY = reader.getSizeY();
>    int pixelType = reader.getPixelType();

The pixel type recorded by the ScanR software is stored in each of the
TIFF files.  The above code retrieves the pixel type stored in the
first TIFF file; later on, that pixel type is assigned to each well
and field.  So for the purposes of importing into OMERO, you should
not need to convert int16 images to uint16 - Bio-Formats will detect
whether or not the images are signed.

The only assumption is that every well and field has the same pixel
type - if you know of a case where that assumption is incorrect,
please let me know.

> A different question would be if the 'real' number of bits used have a place
> in OMERO metada, for example for many microscopes this is 12 bits.

The "real" bit depth is not currently stored.  We do have plans to
record this information in Bio-Formats (see
https://skyking.microscopy.wisc.edu/trac/java/ticket/433); I'm not
sure if there are plans to add this to the OME-XML data model.

Regards,
-Melissa

On Thu, Nov 26, 2009 at 11:27 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hello Melissa,
> Your ScanR importer has loaded tons of datasets in our premises. We are
> concerned that ScanR software is storing signed bit images, but part of the
> code reads:
>
>    reader = new MinimalTiffReader();
>    reader.setId(tiffs[0]);
>    int sizeX = reader.getSizeX();
>    int sizeY = reader.getSizeY();
>    int pixelType = reader.getPixelType();
>
> I cannot say how ScanR tells the sample bit representation, in this lab we
> are used to convert the images from int16 to uint16 before processing them,
> actually thats the way we keep on doing this.
>
> Will be more convenient if the importer would store the proper value, but I
> also would like to ask your opinion, since you are the expert.
>
> A different question would be if the 'real' number of bits used have a place
> in OMERO metada, for example for many microscopes this is 12 bits.
>
> Regards,
>
> --
> Rubén Muñoz
> European Molecular Biology Laboratory
>
>
>
>