bioformats retrieve calibration in JAVA

[Emanuele Martini]

Hi to all,
I am trying to retrieve the calibration of a single series of image usi bioformats api.
How can I do that?
I am doing something like:
ImageProcessorReader r = new ImageProcessorReader( new ChannelMerger(LociPrefs.makeImageReader()));
r.setId(path_file);

r.get...
and here the problems... there are a lot of getmetadata features I don't understand how to arrive to getPixelsPhysicalSizeX()

Could you please hel pme?
Thanks
Emanuele Martini

[Jan Eglinger]

Hi Emanuele,

have a look at this example script by Curtis Rueden:
https://gist.github.com/ctrueden/6282856

After retrieving the metadata object `omeMeta`, this should work for you:
     omeMeta.getPixelsPhysicalSizeX();

See
http://javadoc.imagej.net/Bio-Formats/index.html?ome/xml/meta/MetadataRetrieve.html
for all the method to retrieve metadata.

Hope that helps,
Jan


On 13.10.2015 12:33, Emanuele Martini wrote:

> Hi to all,
> I am trying to retrieve the calibration of a single series of image usi
> bioformats api.
> How can I do that?
> I am doing something like:
> ImageProcessorReader r = new ImageProcessorReader( new
> ChannelMerger(LociPrefs.makeImageReader()));
> r.setId(path_file);
>
> r.get...
> and here the problems... there are a lot of getmetadata features I don't
> understand how to arrive to getPixelsPhysicalSizeX()
>
> Could you please hel pme?
> Thanks
> Emanuele Martini
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Emanuele and Jan,

> After retrieving the metadata object `omeMeta`, this should work for you:
>     omeMeta.getPixelsPhysicalSizeX();

The Bio-Formats API changed to include units in its physical calibrations.
So you have to be careful now that you are working with calibration in the
correct units. I updated the example script to work properly with the
current version Bio-Formats, and to illustrate this.

https://gist.github.com/ctrueden/6282856

Regards,
Curtis

On Tue, Oct 13, 2015 at 7:07 AM, Jan Eglinger <[hidden email]>
wrote:

> Hi Emanuele,
>
> have a look at this example script by Curtis Rueden:
> https://gist.github.com/ctrueden/6282856
>
> After retrieving the metadata object `omeMeta`, this should work for you:
>     omeMeta.getPixelsPhysicalSizeX();
>
> See
> http://javadoc.imagej.net/Bio-Formats/index.html?ome/xml/meta/MetadataRetrieve.html
> for all the method to retrieve metadata.
>
> Hope that helps,
> Jan
>
>
> On 13.10.2015 12:33, Emanuele Martini wrote:
>
>> Hi to all,
>> I am trying to retrieve the calibration of a single series of image usi
>> bioformats api.
>> How can I do that?
>> I am doing something like:
>> ImageProcessorReader r = new ImageProcessorReader( new
>> ChannelMerger(LociPrefs.makeImageReader()));
>> r.setId(path_file);
>>
>> r.get...
>> and here the problems... there are a lot of getmetadata features I don't
>> understand how to arrive to getPixelsPhysicalSizeX()
>>
>> Could you please hel pme?
>> Thanks
>> Emanuele Martini
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Emanuele Martini]

Hi all,
it works thank you all.

see you,
Emanuele Martini