[ome-users] Bits per pixel

[Will Moore]

Hi Mark,

  Sorry - meant to reply earlier.

On 23 Jun 2011, at 16:54, Mark Woodbridge 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.

Hmm - if you want to make sure that all the images in a batch export  
have the same range, you could get the min/max from all of them first,  
then choose a global rendering setting to apply to all images.

However, another problem with using the min/max is that this is the  
range BEFORE projection. After doing the projection you are likely to  
have significant portions of the image become saturated using this  
rendering window? However, if doing this for a whole batch of images,  
it is likely that only the brightest few images would have this problem.

>
> 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?

No, afraid not.
It's not really a "tiff" you're getting but 32 bits (8 each for  
r,g,b,a) of data that can be used for png, jpeg etc.

   Will.


>
> 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
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> 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
>>
>>
>>
>>
>>

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