[ome-users] Bugreport - BioFormats CZIReader gets Dimension Order of CZI wrong

[Curtis Rueden]

Hi Sebastian,

> the dimension order specifies the order in which images are returned,
> not necessarily the order in which they were acquired.

Indeed, although the two match extremely often, since the original idea in
BF was that the dimension order reflects the order of the planes within the
dataset on disk (on a best effort basis -- e.g., dimension orders that do
not start with XY were never supported). Optionally, the DimensionSwapper
can be used to reorder things to a more desirable ordering, if needed --
both for "input dimension order" if BF's detected dimension order is wrong,
and for "output dimension order" if the planes' dim coordinates are right
but you want the 1-dimensional rasterization order to be different.

Regards,
Curtis

On Mon, Mar 16, 2015 at 11:03 AM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> Hi Sebi,
>
> > I think you can ignore my last mail on the dimension order problem for
> now,
> > since this was misconception on my side ...
> >
> >
> > Just to be sure, the dimensio order XYCZT, has nothing to do with the
> order
> > of the actual acquistion order (1st - Channel, 2nd - Z and 3rd Time
> right?
>
> That's correct - the dimension order specifies the order in which images
> are returned, not necessarily the order in which they were acquired.
> For .czi datasets, the dimension order is always XYCZT (for convenience,
> since images can be stored in any order within the file), which
> corresponds to channels first, then Z sections, then timepoints.
>
> Regards,
> -Melissa
>
> On Mon, Mar 16, 2015 at 01:58:10PM +0100, Sebastian Rhode wrote:
> > Hi guys,
> >
> > I think you can ignore my last mail on the dimension order problem for
> now,
> > since this was misconception on my side ...
> >
> >
> > Just to be sure, the dimensio order XYCZT, has nothing to do with the
> order
> > of the actual acquistion order (1st - Channel, 2nd - Z and 3rd Time
> right?
> >
> >
> > Sebi
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150316/fa43dd2d/attachment.html>