Augmenting an ImagePlus with Additional Information
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Augmenting an ImagePlus with Additional Information
 
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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? Michael Ellis Managing Director Digital Scientific UK Ltd. http://www.digitalscientific.co.uk [hidden email] tel: +44(0)1223 329993 fax: +44(0)1223 370040 Sheraton House Castle Park Cambridge CB3 0AX The contents of this e-mail may be privileged and are confidential. It may not be disclosed to or used by anyone other than the addressee(s), nor copied in any way. If received in error, please advise the sender and delete it from your system. |
Antwort: Augmenting an ImagePlus with Additional Information
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Hi,
I have/had the same problem to read some proprietary Tiff files with extra tags whose info should be available later in ImageJ. You can use ImagePlus´ getProperty/setProperty to do this, but I am not sure if these properties will survive duplication (actually I fear they will not), it was not yet important for me! (I also wrote a macro helper function to read these properties) Cheers. Mit freundlichen Grüßen / Best regards Joachim Wesner www.leica-microsystems.com Michael Ellis <michael.ellis@DI GITALSCIENTIFIC.C An O.UK> [hidden email] Gesendet von: Kopie ImageJ Interest Group Thema <[hidden email]. Augmenting an ImagePlus with GOV> Additional Information 22.02.2010 18:21 Bitte antworten an ImageJ Interest Group <[hidden email]. GOV> 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? Michael Ellis Managing Director Digital Scientific UK Ltd. http://www.digitalscientific.co.uk [hidden email] tel: +44(0)1223 329993 fax: +44(0)1223 370040 Sheraton House Castle Park Cambridge CB3 0AX The contents of this e-mail may be privileged and are confidential. It may not be disclosed to or used by anyone other than the addressee(s), nor copied in any way. If received in error, please advise the sender and delete it from your system. ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
Re: Augmenting an ImagePlus with Additional Information
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In reply to this post by Michael Ellis
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 |
Re: Antwort: Augmenting an ImagePlus with Additional Information
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In reply to this post by Joachim Wesner
Joachim, hi
On 22 Feb 2010, at 18:43, Joachim Wesner wrote: > Hi, > > I have/had the same problem to read some proprietary Tiff files with > extra > tags whose info should be available later in ImageJ. > > You can use ImagePlus´ getProperty/setProperty to do this, but I am > not > sure if these properties will survive duplication I just stumbled upon the getProperty/setProperty and wrote a plugin to test this. I can verify that any properties you do NOT survive image duplication. Shame that image duplication does not clone the properties, perhaps there is some good reason for this though? > (actually I fear they will not), it was not yet important for me! (I > also > wrote a macro helper function to read these properties) > > Cheers. > > Mit freundlichen Grüßen / Best regards > > Joachim Wesner > www.leica-microsystems.com Best regards -- Michael Ellis |
Re: Augmenting an ImagePlus with Additional Information
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In reply to this post by Rasband, Wayne (NIH/NIMH) [E]
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] tel: +44(0)1223 329993 fax: +44(0)1223 370040 Sheraton House Castle Park Cambridge CB3 0AX The contents of this e-mail may be privileged and are confidential. It may not be disclosed to or used by anyone other than the addressee(s), nor copied in any way. If received in error, please advise the sender and delete it from your system. |
Antwort: Re: Augmenting an ImagePlus with Additional Information
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In reply to this post by Rasband, Wayne (NIH/NIMH) [E]
Hi Wayne,
>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. This is good news (I must have missed this :-( ), so there is finally a standardized way to save the ROI with the Tiff data! I was looking for this already for some time! Joachim Wesner Projektleiter Optik Technologiesysteme www.leica-microsystems.com ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
Antwort: Re: Antwort: Augmenting an ImagePlus with Additional Information
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In reply to this post by Michael Ellis
>I just stumbled upon the getProperty/setProperty and wrote a plugin to
>test this. I can verify that any properties you do NOT survive image >duplication. Shame that image duplication does not clone the >properties, perhaps there is some good reason for this though? I think one should not blame ImageJ developers for this, AFAIK the usual approach is to only do what is "save", it is generally nontrivial to duplicate an arbitrary composed object, there is no "correct" way to do this (Shallow copy vs. Deep copy etc.), without knowing how the copy will be used later, see the discussions about cloning in Java. Mit freundlichen Grüßen / Best regards www.leica-microsystems.com ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
Re: Antwort: Re: Antwort: Augmenting an ImagePlus with Additional Information
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Joachim,
Oh no blame! Imagej is the best thing since sliced bread for a million reasons. And yes, duplication (and persistence) of composite object data is a non trivial. We've used a variety of approached in our own products over the years. Anyway, cannot complain (as you say), within a day I've been able to write the bare bones of a plugin that can read our kartotype files that contain arbitrary multiplane and multi(overlapping)frame images and load up the chromosome boundaries into the ROI manager. Imagine doing all that from scratch without ImageJ -- no siree no blame or complaints from over here! Regards -- Michael On 22 Feb 2010, at 19:22, Joachim Wesner wrote: >> I just stumbled upon the getProperty/setProperty and wrote a plugin >> to >> test this. I can verify that any properties you do NOT survive image >> duplication. Shame that image duplication does not clone the >> properties, perhaps there is some good reason for this though? > > I think one should not blame ImageJ developers for this, AFAIK the > usual > approach is to only > do what is "save", it is generally nontrivial to duplicate an > arbitrary > composed object, there is > no "correct" way to do this (Shallow copy vs. Deep copy etc.), without > knowing how the copy > will be used later, see the discussions about cloning in Java. > > Mit freundlichen Grüßen / Best regards > > www.leica-microsystems.com > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ Michael Ellis Managing Director Digital Scientific UK Ltd. http://www.digitalscientific.co.uk [hidden email] tel: +44(0)1223 329993 fax: +44(0)1223 370040 Sheraton House Castle Park Cambridge CB3 0AX The contents of this e-mail may be privileged and are confidential. It may not be disclosed to or used by anyone other than the addressee(s), nor copied in any way. If received in error, please advise the sender and delete it from your system. |
Re: Antwort: Augmenting an ImagePlus with Additional Information
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In reply to this post by Michael Ellis
On Feb 22, 2010, at 1:56 PM, Michael Ellis wrote:
> Joachim, hi > > On 22 Feb 2010, at 18:43, Joachim Wesner wrote: > >> Hi, >> >> I have/had the same problem to read some proprietary Tiff files with >> extra >> tags whose info should be available later in ImageJ. >> >> You can use ImagePlus´ getProperty/setProperty to do this, but I am >> not >> sure if these properties will survive duplication > > I just stumbled upon the getProperty/setProperty and wrote a plugin to > test this. I can verify that any properties you do NOT survive image > duplication. Shame that image duplication does not clone the > properties, perhaps there is some good reason for this though? The "Info" image property (a String) does survive image duplication. It is also preserved when the image is saved in TIFF format. -wayne > (actually I fear they will not), it was not yet important for me! (I >> also >> wrote a macro helper function to read these properties) > >> >> Cheers. >> >> Mit freundlichen Grüßen / Best regards >> >> Joachim Wesner >> www.leica-microsystems.com > > Best regards -- Michael Ellis |
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