<div class="gmail_quote">Hi everyone,<br><br>On Mon, Sep 7, 2009 at 6:59 AM, Nick Perry <span dir="ltr"><<a href="mailto:nperry@stanford.edu">nperry@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I'm
converting a file format to OME-TIFF, and I was wondering if there were
any sort of standards for the TIFF 'part' of the OME-TIFF. For example:<br><br>1. is it suggested to have IFDs before or after the raw image data they describe?<br>
2. is there a preferred number for RowsPerStrip? For example, should
RowsPerStrip just be 1? Should each image plane just be a single strip?<br></blockquote><div><br>I
answered these questions earlier on the list and/or privately to Nick, but thought I would repost the answers here, for the thread
archive.<br><br>
-Curtis<br>
<br></div></div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Curtis Rueden</b> <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span><br>
Date: Tue, Sep 8, 2009 at 1:41 PM<br>Subject: Re: [ome-devel] Required TIFF IFD Fields in OME-TIFF?<br>To: Nick Perry <<a href="mailto:nperry@stanford.edu" target="_blank">nperry@stanford.edu</a>><br>Cc: <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<br><div class="gmail_quote">Hi Nick,<br><div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Of
perhaps more importance: does OME care about IFDs? Are there required
IFD data? Or does the completeness of my IFDs only make the file more
compatible with TIFF readers and not really effect OME? Like, could I
just skip the details in the TIFF IFDs and just have things like
ImageWidth, ImageLength, etc, which I'm sure the bio-formats tools need
to correctly parse the data?</blockquote></div><div><br>OME
does not specifically care about any IFD values, no -- at least, not
any above and beyond what would normally be required for a regular
TIFF. You should populate exactly what you would normally populate if
the file were not OME-TIFF. Any overlap between OME metadata and TIFF
IFD values (SizeX vs. ImageWidth, SizeY vs. ImageHeight, etc.) should
be consistent -- if it is not, Bio-Formats will issue a warning message
and the resultant behavior may not be what you want.<br>
</div></div><br>-Curtis<br></div><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Curtis Rueden</b> <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a>></span><br>
Date: Tue, Sep 8, 2009 at 4:39 PM<br>Subject: Re: [ome-devel] Required TIFF IFD Fields in OME-TIFF?<br>To: Nick Perry <<a href="mailto:nperry@stanford.edu">nperry@stanford.edu</a>><br><br>Hi Nick,<br><br><div class="gmail_quote">
<div class="im"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Quick
question - as far as RowsPerStrip is concerned, I see in one of your
examples from the LOCI site that for an image (tubhiswt_C1.ome.tif,
from the 3D) with 512 as ImageLength (y = 512), you also put 512 as the
number of rows per strip (giving StripByteCount a value of 262,144). Do
you recommend putting all the rows of an image plane in each strip?
Does it make a difference? I see on the TIFF6 specification from adobe
that they recommend each strip having about 8k bytes. Does it actually
affect efficiency in reading/buffering?<br></blockquote></div><div><br>Are
you coding a TIFF writer from scratch? If working in C/C++, I would
suggest using libtiff, and if using Java, I would suggest using the
Bio-Formats TiffWriter implementation.<br>
<br>That said, I'm sure the performance depends on the TIFF reader
implementation when reading the file back in. For a naive TIFF reader,
it might suck in one strip at a time, so you might want your strip size
to equal your buffer size. In the past 8K was a good buffer size, but
these days something more like 256K is better (at least in my
experience with empirical tests). But off the top of the head I'm not
sure what our TIFF writer does -- it might always put all the rows in
one strip. I wouldn't worry about it too much though unless you have
absolutely huge image planes.<br>
<br></div></div>-Curtis<br>
</div><br>