[ome-users] dm4 imports with um scale instead of nm

[Melissa Linkert]

Hi,

> > But if it's a free text field, we would need to be able to do general
> > unit interconversion, which is a bigger problem to tackle.
> 
> Just in case it wasn't clear from my previous reply: we have solved this
> problem in ImgLib2 and SCIFIO. By migrating to the new SCIFIO API,
> Bio-Formats will be able to take full advantage of it.

We appreciate the efforts that the SCIFIO team have made on this front.
Please note, however, that a plan and timeline for using SCIFIO within
Bio-Formats has not been established, and realistically we don't
anticipate this happening for many months yet.  Anyone needing the
functionality mentioned by Curtis will need to use SCIFIO directly,
with the caveat that the OME team cannot provide support for doing so.

Regards,
-Melissa

On Tue, Nov 05, 2013 at 10:35:21AM -0600, Curtis Rueden wrote:
> Hi Roger,
> 
> > But if it's a free text field, we would need to be able to do general
> > unit interconversion, which is a bigger problem to tackle.
> 
> Just in case it wasn't clear from my previous reply: we have solved this
> problem in ImgLib2 and SCIFIO. By migrating to the new SCIFIO API,
> Bio-Formats will be able to take full advantage of it.
> 
> Regards,
> Curtis
> 
> 
> On Mon, Nov 4, 2013 at 4:06 AM, Roger Leigh <r.leigh at dundee.ac.uk> wrote:
> 
> > On 04/11/2013 06:26, Ralph Sperling wrote:
> >
> >>
> >> Dear all,
> >>
> >> if there is good reason to stick with microns everywhere, nanometers
> >> could be taken into account by just dividing the pixel size by 1000, I
> >> guess this is exactly what Stephane suggested.
> >>
> >
> > In the short term, this is exactly what the reader should do if the unit
> > is recorded as nm.  However, the complexity of doing this depends upon
> > how the units are stored; for readers which store the unit as an
> > enumeration, the conversions can be hardcoded.  But if it's a free text
> > field, we would need to be able to do general unit interconversion,
> > which is a bigger problem to tackle.
> >
> > In the longer term, we're looking at adding units to the data model so
> > that we can store nm and other units natively.
> >
> >
> >  At the moment I am doing similar things with a macro - is there a way to
> >> do custom adjustments automagically, e.g. always after importing .dm4
> >> files? This would be a convenient solution for the moment.
> >>
> >
> > This is certainly possible.  If the image filename ends with ".dm4",
> > then you just need to check for that and then after the image has been
> > imported, call:
> >
> >   run("Set Scale...", "distance=x known=y pixel=1 unit=nm");
> >
> > but getting the scale doesn't appear to be exposed in the macro language
> > from my reading of the documentation; you might need to call
> >
> >   toScaled(x,y)
> >
> > with some sample numbers, e.g. x=1000, y=1000, to compute the scale
> > factor, then adjust it from µm to nm, before calling "Set Scale".
> >
> > There may be a better way of doing this; if so, I hope one of the ImageJ
> > experts reading the list could suggest an alternative approach.
> >
> >
> > Regards,
> > Roger
> >
> > --
> > Dr Roger Leigh -- Open Microscopy Environment
> > Wellcome Trust Centre for Gene Regulation and Expression,
> > College of Life Sciences, University of Dundee, Dow Street,
> > Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >

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