[ome-devel] ScanR importer bit representation

[Rubén Muñoz]

>
> Hi Ruben,

Hi Melissa, I understand that mine was not an ScanR specific question,  
but I have to detail a bit more what I believe an issue.

> 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.

With images from this microscope Pixel type = uint16 is auto detected,  
but they are all signed 16 bit, we know this with precision.

Then the files are not properly auto-detected, or the files are not  
consistent themselves, next is the output of ./showinf

Checking file format [Olympus ScanR]
...
Series count = 54
Series #0:
	Image count = 25
	RGB = false (1)
	Interleaved = false
	Indexed = false (true color)
	Width = 1344
	Height = 1024
	SizeZ = 1
	SizeT = 25
	SizeC = 1
	Thumbnail size = 128 x 97
	Endianness = intel (little)
	Dimension order = XYCTZ (uncertain)
	Pixel type = uint16
	Metadata complete = false
	Thumbnail series = false


16 signed bit images display completely out of range, far too bright  
only in light grey (also with ./showinf).

Can we do something about it, to have "int16" stored would be correct.

>
> 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

All them are signed so far.


Thanks for your understanding,

Ruben

>
> 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
>>
>>
>>
>>

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