[ome-users] relationship between Pixels/SizeC and TiffData/FirstC

[Curtis Rueden]

Hi Ming,


>
> 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?
>

The Size[XYZCT] elements of Pixels are required, and define the dimensional
extents of your data.

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.

See the OME-TIFF specification page for details:

https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-specification


>
> 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?
>

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.

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.

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.

The OME-TIFF tubhiswt sample dataset may also serve as a useful
illustration:

https://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data

Regards,
Curtis


On Mon, Jul 2, 2012 at 10:52 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Ming,
>
>
>>
>> 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?
>>
>> 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?
>>
>
> 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.
>
> -Curtis
>
>
> On Mon, Jul 2, 2012 at 8:31 AM, Ming Gao <MGao at thorlabs.com> wrote:
>
>> Hello,
>>
>> 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?
>>
>> 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?
>>
>> Regards,
>> -Ming
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
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