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

[Curtis Rueden]

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
>
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