Posted by
Michael Ellis on
URL: http://imagej.273.s1.nabble.com/Augmenting-an-ImagePlus-with-Additional-Information-tp3689248p3689256.html
Wayne, thanks, I look into that (possibly tonight).
A couple of questions:
- All the individual polygons (one for each chromosome) need to be
individually accessible, does the overlay allow for multiple
individually accessible polygons?
- I also have other metrics that needs to be "taken care of"; the
chromosome angle of rotation, centromere position and other such bits
and bytes, any ideas?
P.S. I greatly appreciate the amazing work and your impressively
timely replies queries on this forum.
Regards -- Michael Ellis
On 22 Feb 2010, at 18:50, Rasband Wayne wrote:
> On Feb 22, 2010, at 12:21 PM, Michael Ellis <
[hidden email]
> > wrote:
>
>> Augmenting an ImagePlus with Additional Information
>>
>> I am writing an ImageJ plugin to read our proprietary file format.
>> Our
>> files are karyotyping files that contain zipped up TIFF files,
>> polygon
>> data describing the chromosome boundaries and various other metrics.
>>
>> So far I can load the image files and I'm adding the list of polygon
>> boundaries as PolygonRoi's to the ROIManager. However, if I use our
>> plugin to load a s second karyotype file, then I have either to
>> append
>> to, or replace the contents of the ROIManager. I'd prefer to
>> associate
>> the list of PolygonRoi's with the image.
>>
>> So how best to do this?
>>
>> Subclassing the ImagePlus might work, but I'm not a fan of type
>> casting; I suspect that it would have gotchas like having ImageJ's
>> "Duplicate" command lose the additional information.
>>
>> Is there any other robust means of augmenting an image with
>> additional
>> information?
>
> Add the polygon boundaries to the image as an overlay (requires
> v1.43). Overlays can be transferred to the ROI Manager, easily
> retrieved using ImagePlus.getOverlay(), and they are saved with the
> image when saving in TIFF format. The Duplicate command will
> preserve overlays in the next daily build.
>
> -wayne
Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk[hidden email]
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fax: +44(0)1223 370040
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