Hi everyone,<br><br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">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.<br></blockquote>
<br>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:<br><br> /**<br>
* Gets the number of valid bits per pixel. The number of valid bits per<br> * pixel is always less than or equal to the number of bits per pixel<br> * that correspond to {@link #getPixelType()}.<br> */<br> int getBitsPerPixel();<br>
<br>Perhaps we should add a field to the OME-XML schema to record this value in a standard way?<br><br>Regards,<br>Curtis<br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 10:54 AM, Mark Woodbridge <span dir="ltr"><<a href="mailto:m.woodbridge@imperial.ac.uk">m.woodbridge@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Ok. It's using uint16. I think all our Zeiss images are 12-bit.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Similarly (but less important), is there a way to specify the bit depth when using renderingEngine.<u></u>renderProjectedAsPackedInt so that I can produce a 12 bit (rather than 8 bit) tiff?<br><font color="#888888">
<br>
Mark.</font><div><div></div><div class="h5"><br>
<br>
On 23/06/11 16:40, Will Moore wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Mark,<br>
<br>
I have an idea what the problem is:<br>
OMERO doesn't support 12 bits:<br>
<br>
omero=# select * from pixelstype;<br>
id | permissions | value | external_id | bitsize<br>
----+-------------+-----------<u></u>-----+-------------+---------<br>
1 | -35 | bit | | 1<br>
2 | -35 | int8 | | 8<br>
5 | -35 | uint8 | | 8<br>
3 | -35 | int16 | | 16<br>
4 | -35 | int32 | | 32<br>
6 | -35 | uint16 | | 32<br>
7 | -35 | uint32 | | 32<br>
8 | -35 | float | | 32<br>
9 | -35 | double | | 64<br>
10 | -35 | complex | | 64<br>
11 | -35 | double-complex | | 128<br>
(11 rows)<br>
<br>
<br>
Can you see what's the pixels type in the database for those images<br>
E.g. psql using imageId...<br>
# select * from pixelstype where id = (select pixelstype from pixels<br>
where image=9986);<br>
(or maybe it's displayed in Insight too)?<br>
<br>
Probably 16 bits??<br>
<br>
Not sure what your best solution is here.<br>
I guess you've not seen this before since you haven't processed any 12<br>
bit images before?<br>
<br>
Not sure the best strategy here.<br>
Would it work for you to simply use the min and max pixel values of<br>
the source image, same as Insight is doing with Min/Max?<br>
<br>
<br>
Will.<br>
<br>
<br>
<br>
On 23 Jun 2011, at 16:08, Mark Woodbridge wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I have a set of lsm files. Bio-Formats showinf says that they have<br>
'Valid bits per pixel = 12'. But when I go to Preview> Full Range<br>
in Insight it sets the maximum to 65535, even though Min/Max gives<br>
0-4095 (as I would expect).<br>
<br>
Is this correct? I have an export script that uses<br>
renderingEngine.<u></u>getPixelsTypeUpperBound to set the channel window<br>
for projection and it similarly returns 65535, meaning that the<br>
resultant projection is very dark.<br>
<br>
Mark.<br>
<br>
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</blockquote>
<br>
William Moore<br>
Wellcome Trust Centre for Gene Regulation& Expression<br>
College of Life Sciences<br>
MSI/WTB/JBC Complex<br>
University of Dundee<br>
Dow Street<br>
Dundee DD1 5EH<br>
United Kingdom<br>
<br>
Phone 01382 386364<br>
<a href="http://openmicroscopy.org" target="_blank">http://openmicroscopy.org</a><br>
<br>
<br>
<br>
<br>
<br>
</blockquote>
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