[ome-users] Bits per pixel

[Mark Woodbridge]

Ok. It's using uint16. I think all our Zeiss images are 12-bit.

I'm not sure whether it's safe to use min/max because if the exported 
images are used in batch processing then each image will have a 
different range.

I might try to pull the original metadata from OMERO ("DataChannel # 
Bits Per Sample") to get the real depth, or make a guess based on the 
min/max values unless anyone has a more elegant solution.

Similarly (but less important), is there a way to specify the bit depth 
when using renderingEngine.renderProjectedAsPackedInt so that I can 
produce a 12 bit (rather than 8 bit) tiff?

Mark.

On 23/06/11 16:40, Will Moore wrote:
> Hi Mark,
>
> I have an idea what the problem is:
> OMERO doesn't support 12 bits:
>
> omero=# select * from pixelstype;
>    id | permissions |     value      | external_id | bitsize
> ----+-------------+----------------+-------------+---------
>     1 |         -35 | bit            |             |       1
>     2 |         -35 | int8           |             |       8
>     5 |         -35 | uint8          |             |       8
>     3 |         -35 | int16          |             |      16
>     4 |         -35 | int32          |             |      32
>     6 |         -35 | uint16         |             |      32
>     7 |         -35 | uint32         |             |      32
>     8 |         -35 | float          |             |      32
>     9 |         -35 | double         |             |      64
>    10 |         -35 | complex        |             |      64
>    11 |         -35 | double-complex |             |     128
> (11 rows)
>
>
> Can you see what's the pixels type in the database for those images
> E.g. psql using imageId...
> # select * from pixelstype where id = (select pixelstype from pixels
> where image=9986);
> (or maybe it's displayed in Insight too)?
>
> Probably 16 bits??
>
> Not sure what your best solution is here.
> I guess you've not seen this before since you haven't processed any 12
> bit images before?
>
> Not sure the best strategy here.
> Would it work for you to simply use the min and max pixel values of
> the source image, same as Insight is doing with Min/Max?
>
>
>     Will.
>
>
>
> On 23 Jun 2011, at 16:08, Mark Woodbridge wrote:
>
>> Hi,
>>
>> I have a set of lsm files. Bio-Formats showinf says that they have
>> 'Valid bits per pixel = 12'. But when I go to Preview>  Full Range
>> in Insight it sets the maximum to 65535, even though Min/Max gives
>> 0-4095 (as I would expect).
>>
>> Is this correct? I have an export script that uses
>> renderingEngine.getPixelsTypeUpperBound to set the channel window
>> for projection and it similarly returns 65535, meaning that the
>> resultant projection is very dark.
>>
>> Mark.
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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>
> William Moore
> Wellcome Trust Centre for Gene Regulation&  Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> Phone 01382 386364
> http://openmicroscopy.org
>
>
>
>
>