[ome-users] Bits per pixel

[Curtis Rueden]

Hi everyone,

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.
>

This idea of "valid bits per pixel" comes up a fair amount, and is distinct
from the storage bit depth—particularly for 12-bit data. Bio-Formats already
supports reporting this information:

  /**
   * Gets the number of valid bits per pixel. The number of valid bits per
   * pixel is always less than or equal to the number of bits per pixel
   * that correspond to {@link #getPixelType()}.
   */
  int getBitsPerPixel();

Perhaps we should add a field to the OME-XML schema to record this value in
a standard way?

Regards,
Curtis

On Thu, Jun 23, 2011 at 10:54 AM, Mark Woodbridge <
m.woodbridge at imperial.ac.uk> wrote:

> 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.
>>>
>>> ______________________________**_________________
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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
>>
>>
>>
>>
>>
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