Hi Ming,<div><div> </div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>I have a question about the intentions of the SizeC (and SizeT, SizeX, etc) and the FirstC ( and FirstT, FirstX, etc). Does a tiff need to have the number of attributes of TiffData/FirstC indicated by the value of Pixels/SizeC? For example, if I have SizeC=3, do I have to have 3 attributes, where FirstC=0, FirstC=1, FirstC=2?<br>
</blockquote><div><br></div><div><div>The Size[XYZCT] elements of Pixels are required, and define the dimensional extents of your data.</div></div><div><br></div><div>The First[CTZ] elements are only used if you are writing OME-TIFF files, and define the mapping from TIFF IFD elements to the corresponding planes in the 5D OME data structure.</div>
<div><br></div><div>See the OME-TIFF specification page for details:</div><div> <a href="https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-specification">https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-specification</a></div>
<div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>I also need to use Plane/TheT, Plane/TheC and Plane/TheZ. Should they be equal to the values of FirstT, FirstC, FirstZ for the plane, or equal to 0, if I only have one plane for each tiff file?<br></blockquote><div><br>
</div><div>For the Plane elements, there is no promise that they appear in any particular order, hence the need for The[CTZ] attributes. If you want to be "nice" you can rasterize the Plane elements in the same dimension order as that defined by Pixels's DimensionOrder attribute, but again, it is not a requirement.</div>
<div><br></div><div>The number of TIFF files in the dataset is irrelevant to Plane's The[CTZ] elements; rather, those coordinates should point to the plane's coordinates in the 5D OME structure.</div><div><br></div>
<div>If you haven't already, I suggest reading the OME-TIFF specification page (linked above). In particular, if you have multiple TIFF files, it is crucial to read and understand the "Distributing an image sequence across multiple OME-TIFF files" section.</div>
<div><br></div>
</div></div><div>The OME-TIFF tubhiswt sample dataset may also serve as a useful illustration:</div><div> <a href="https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data">https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data</a></div>
<div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><div><br><div class="gmail_quote">On Mon, Jul 2, 2012 at 10:52 AM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ming,<div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br></blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
I have a question about the intentions of the SizeC (and SizeT, SizeX, etc) and the FirstC ( and FirstT, FirstX, etc). Does a tiff need to have the number of attributes of TiffData/FirstC indicated by the value of Pixels/SizeC? For example, if I have SizeC=3, do I have to have 3 attributes, where FirstC=0, FirstC=1, FirstC=2?<br>
<br>I also need to use Plane/TheT, Plane/TheC and Plane/TheZ. Should they be equal to the values of FirstT, FirstC, FirstZ for the plane, or equal to 0, if I only have one plane for each tiff file?<br></blockquote><div><br>
</div></div><div>It sounds like you are asking about OME-TIFF, so a better mailing list would be OME-users. Let's discuss there instead. I will reply back and CC that list rather than ImageJ.</div><span><font color="#888888"><div>
<br></div><div>-Curtis</div></font></span><div><div>
<div> </div><br><div class="gmail_quote">On Mon, Jul 2, 2012 at 8:31 AM, Ming Gao <span dir="ltr"><<a href="mailto:MGao@thorlabs.com" target="_blank">MGao@thorlabs.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I have a question about the intentions of the SizeC (and SizeT, SizeX, etc) and the FirstC ( and FirstT, FirstX, etc). Does a tiff need to have the number of attributes of TiffData/FirstC indicated by the value of Pixels/SizeC? For example, if I have SizeC=3, do I have to have 3 attributes, where FirstC=0, FirstC=1, FirstC=2?<br>
<br>
I also need to use Plane/TheT, Plane/TheC and Plane/TheZ. Should they be equal to the values of FirstT, FirstC, FirstZ for the plane, or equal to 0, if I only have one plane for each tiff file?<br>
<br>
Regards,<br>
-Ming<br>
<br>
<br>
--<br>
ImageJ mailing list: <a href="http://imagej.nih.gov/ij/list.html" target="_blank">http://imagej.nih.gov/ij/list.html</a><br>
</blockquote></div><br></div></div></div>
</blockquote></div><br></div></div>