[ome-users] Bits per pixel

[Will Moore]

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.
>
> _______________________________________________
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> 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