Zooming and smoothing
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My first post!
When I zoom on my image in imagej, it becomes highly pixelated. When i do the same on another program the image does not. I presume that the other program is interpolating pixels or smoothing the image in some way. I need ImageJ to do the same. The smooth function doesnt add more pixels which is what i need it to do. Any ideas? Many thanks |
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Hash: SHA1 Open Edit>Options>Appearance and check Interpolate Zoomed Images. Volker flettster a écrit : > My first post! > > When I zoom on my image in imagej, it becomes highly pixelated. When i do > the same on another program the image does not. > > I presume that the other program is interpolating pixels or smoothing the > image in some way. > > I need ImageJ to do the same. The smooth function doesnt add more pixels > which is what i need it to do. > > Any ideas? > > Many thanks Version: GnuPG v1.4.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFJt8HCxZKX7A/4oMERAhpGAKDCCk80R3OO25OjMRu1fe8/SDK1FwCgiqvc jmLK/vJn6bAH/RX1qXpHbHU= =STni -----END PGP SIGNATURE----- -- passerelle antivirus du campus CNRS de Montpellier -- |
Re: Zooming and smoothing
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In reply to this post by flettster
Edit/Options then check "Interpolate Zoomed Images"
Bob Z -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of flettster Sent: Wednesday, March 11, 2009 9:20 AM To: [hidden email] Subject: Zooming and smoothing My first post! When I zoom on my image in imagej, it becomes highly pixelated. When i do the same on another program the image does not. I presume that the other program is interpolating pixels or smoothing the image in some way. I need ImageJ to do the same. The smooth function doesnt add more pixels which is what i need it to do. Any ideas? Many thanks -- View this message in context: http://n2.nabble.com/Zooming-and-smoothing-tp2461280p2461280.html Sent from the ImageJ mailing list archive at Nabble.com. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. |
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In reply to this post by flettster
On Wednesday 11 March 2009 13:20:14 flettster wrote:
> When I zoom on my image in imagej, it becomes highly pixelated. > When i do > the same on another program the image does not. > I presume that the other program is interpolating pixels or smoothing the > image in some way. > I need ImageJ to do the same. The smooth function doesnt add more pixels > which is what i need it to do. You can check the option: Edit>Options>Appearance>Interpolate Zoomed Images Or Add this line to the AutoRun macro in /macros/StartupMacros: run("Appearance...", "interpolate"); Cheers G |
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It is amazing how easy something is when you know how!!
Thanks
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I have a new problem now. The image looks great - just what i needed However, the selection tool and thresholding are still pixelated. Is there a way of interpolating for these too? Thanks
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On Wednesday 11 March 2009 15:00:09 flettster wrote:
> However, the selection tool and thresholding are still pixelated. > > Is there a way of interpolating for these too? No, there isn't. You need to remember that you are working on a discrete space. G. |
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oh dear
This is difficult because i have a fairly rounded structure, then I draw a free hand selection and it creates a zigzag in pixels which makes it impossible to follow the round. Likewise for the thresholding - the pixelation is very obvious. Is there a way of cheating by creating a new image which includes the interpolated pixels? I need my selections and thresholding to look nice as well as actually create measurements in order for people to buy in to the technique! Thanks
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Dear,
there might be a fundamental misunderstanding: ImageJ is meant as a tool for scientific image analysis and not for nice looking pictures and image cosmetics! Best Herbie >oh dear > >This is difficult because i have a fairly rounded structure, then I draw a >free hand selection and it creates a zigzag in pixels which makes it >impossible to follow the round. Likewise for the thresholding - the >pixelation is very obvious. > >Is there a way of cheating by creating a new image which includes the >interpolated pixels? > >I need my selections and thresholding to look nice as well as actually >create measurements in order for people to buy in to the technique! > >Thanks > >Gabriel Landini wrote: >> >> On Wednesday 11 March 2009 15:00:09 flettster wrote: >>> However, the selection tool and thresholding are still pixelated. >>> >>> Is there a way of interpolating for these too? >> >> No, there isn't. You need to remember that you are working on a discrete >> space. >> > > G. |
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In reply to this post by flettster
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Hash: SHA1 Keep in mind that however smooth it will look the zigzag thing is just the reality and defines what you will measure. I see two possibilities to make it look smoother: 1. scale up the image with the interpolation option selected (Image>Scale) 2. Have a look at the ObjectJ plugin (http://simon.bio.uva.nl/objectj/). I think it can do what you want, but I'm not sure. Maybe someone else can confirm this? Volker flettster a écrit : > oh dear > > This is difficult because i have a fairly rounded structure, then I draw a > free hand selection and it creates a zigzag in pixels which makes it > impossible to follow the round. Likewise for the thresholding - the > pixelation is very obvious. > > Is there a way of cheating by creating a new image which includes the > interpolated pixels? > > I need my selections and thresholding to look nice as well as actually > create measurements in order for people to buy in to the technique! > > Thanks > > > Gabriel Landini wrote: >> On Wednesday 11 March 2009 15:00:09 flettster wrote: >>> However, the selection tool and thresholding are still pixelated. >>> >>> Is there a way of interpolating for these too? >> No, there isn't. You need to remember that you are working on a discrete >> space. >> >> G. >> >> > Version: GnuPG v1.4.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFJt93+xZKX7A/4oMERAn1aAKDsfZdBQ1T6oZA+9hMbzEwHhAp7swCg2bah 0OaPlht/Sqf11zutaAQLO4I= =JR1J -----END PGP SIGNATURE----- -- passerelle antivirus du campus CNRS de Montpellier -- |
Antwort: Re: Zooming new problem
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In reply to this post by Gluender-2
ImageJ Interest Group <[hidden email]> schrieb am 11.03.2009 16:44:54:
> Dear, > > there might be a fundamental misunderstanding: > > ImageJ is meant as a tool for scientific image analysis and not for > nice looking pictures and image cosmetics! > YES! > >Is there a way of cheating by creating a new image which includes the > >interpolated pixels? > > HOWEVER, some people talk about "superresolution" and "subpixels" for scientific use.... What you can do, I do not know if it helps your case, also because I have no experinece how good ImageJs interpolation is, you can create a scaled up version of your original image (Image/Scale...", there is an "interpolation" option JW ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
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In reply to this post by Gluender-2
I understand that it is to be used for making scientific measurements and that is what I need to use it for. The problem is that if those measurements dont look believable or robust to everyone else, they wont believe that the technique itself is believable or robust unless you spend an hour explaining why it is so. Sometimes, it is better to eliminate this step, if it makes no difference to the actual measurement - as in this case.
Thanks for your comment though.
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The scaling option worked perfectly for what i need.
Thanks |
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In reply to this post by flettster
On Wednesday 11 March 2009 15:59:31 flettster wrote:
> I understand that it is to be used for making scientific measurements and > that is what I need to use it for. The problem is that if those > measurements dont look believable or robust to everyone else, they wont > believe that the technique itself is believable or robust unless you spend > an hour explaining why it is so. > > Sometimes, it is better to eliminate this > step, if it makes no difference to the actual measurement - as in this > case. Forget ImageJ, you need to read this, and urgently: http://jcb.rupress.org/cgi/content/full/166/1/11 Cheers, G |
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In reply to this post by flettster
Sorry Sir,
but what you intend to do is invent pictorial information that is not present in your original data (I won't discuss super-resolution here) and you yourself used the term "cheating". Why not show pixelated data if it represents the given image resolution? Is an image at its original resolution not believable or robust? I don't get the point from what you are saying. Best wishes Herbie >I understand that it is to be used for making scientific measurements and >that is what I need to use it for. The problem is that if those measurements >dont look believable or robust to everyone else, they wont believe that the >technique itself is believable or robust unless you spend an hour explaining >why it is so. Sometimes, it is better to eliminate this step, if it makes no >difference to the actual measurement - as in this case. > >Thanks for your comment though. > > >Gluender-2 wrote: >> >> Dear, >> >> there might be a fundamental misunderstanding: >> >> ImageJ is meant as a tool for scientific image analysis and not for >> nice looking pictures and image cosmetics! >> >> Best >> >> Herbie >> >>>oh dear >>> >>>This is difficult because i have a fairly rounded structure, then I draw a >>>free hand selection and it creates a zigzag in pixels which makes it >>>impossible to follow the round. Likewise for the thresholding - the >>>pixelation is very obvious. >>> >>>Is there a way of cheating by creating a new image which includes the >>>interpolated pixels? >>> >>>I need my selections and thresholding to look nice as well as actually >>>create measurements in order for people to buy in to the technique! >>> >>>Thanks >>> >>>Gabriel Landini wrote: >>>> >>>> On Wednesday 11 March 2009 15:00:09 flettster wrote: >>>>> However, the selection tool and thresholding are still pixelated. >>>>> >>>>> Is there a way of interpolating for these too? >>>> >>>> No, there isn't. You need to remember that you are working on a >>>> discrete >>>> space. >>>> > >> > G. |
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All your points are well taken. I agree actually
I just need it to look smooth in this case. Thanks Andy
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In reply to this post by Gluender-2
Herbie, Gabriel, Volker, and everyone,
I prepare my acoustic images by computing them on a coarse grid (related to the phased array resolution) and then interpolating to a finer grid for presentation. I found that the bilinear interpolation in ImageJ was not doing what I needed, so I wrote a bicubic interpolation code by extending the FloatProcessor class and overriding getInterpolatedPixel. There are other bicubic interpolation plugins available for ImageJ, including an example from the Burger and Burge book, but in each case the interpolation is part of something else, not a direct effort to extend ImageJ. I posted my code on my web site last year in the hopes that someone would run with it by implementing the algorithm for the other image types and offering it to Wayne. I was a little tentative because I was not sure that my somewhat invented algorithm would work out. I've been using it a lot, and it seems to be perfect for my needs. If it is time for ImageJ to go bicubic, here is a simple path for it. I do not have time to do the coding right now. Bob Robert Dougherty, Ph.D. President, OptiNav, Inc. 4176 148th Ave. NE Redmond, WA 98052 (425)891-4883 FAX (425)467-1119 www.optinav.com [hidden email] |
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Hi Bob,
as you mention, we have listed a number of different interpolation methods in the source section of our website (imagingbook.com), including cubic and other spline methods. I particularly recommend the Catmull-Rom formulation for good results. I can also send you code for a Lanczos interpolator, which has no visible advantage though. All these methods are pretty standard and implemented by stand-alone code that could be copied directly into ImageProcessor's getInterpolatedPixel() method and selected using a suitable mode switch. Wilhelm ________________________________ Von: ImageJ Interest Group im Auftrag von Robert Dougherty Gesendet: Mi 11.03.2009 20:25 An: [hidden email] Betreff: Re: Zooming new problem Herbie, Gabriel, Volker, and everyone, I prepare my acoustic images by computing them on a coarse grid (related to the phased array resolution) and then interpolating to a finer grid for presentation. I found that the bilinear interpolation in ImageJ was not doing what I needed, so I wrote a bicubic interpolation code by extending the FloatProcessor class and overriding getInterpolatedPixel. There are other bicubic interpolation plugins available for ImageJ, including an example from the Burger and Burge book, but in each case the interpolation is part of something else, not a direct effort to extend ImageJ. I posted my code on my web site last year in the hopes that someone would run with it by implementing the algorithm for the other image types and offering it to Wayne. I was a little tentative because I was not sure that my somewhat invented algorithm would work out. I've been using it a lot, and it seems to be perfect for my needs. If it is time for ImageJ to go bicubic, here is a simple path for it. I do not have time to do the coding right now. Bob Robert Dougherty, Ph.D. President, OptiNav, Inc. 4176 148th Ave. NE Redmond, WA 98052 (425)891-4883 FAX (425)467-1119 www.optinav.com [hidden email] |
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Hi,
On Wed, 11 Mar 2009, Burger Wilhelm wrote: > as you mention, we have listed a number of different interpolation > methods in the source section of our website (imagingbook.com), > including cubic and other spline methods. I particularly recommend the > Catmull-Rom formulation for good results. I can also send you code for a > Lanczos interpolator, which has no visible advantage though. > > All these methods are pretty standard and implemented by stand-alone > code that could be copied directly into ImageProcessor's > getInterpolatedPixel() method and selected using a suitable mode switch. Usually I would not say anything, but since we discussed clean design earlier: I think it would not be appropriate to put this method into ImageProcessor (think MVC), at least not with a global switch as to which interpolation method is actually used. Ciao, Dscho |
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Oh sure, but this would be in line with the current implementation and would not break existing code. The switch would not be global but "private" to the individual ImageProcessor (with set-method etc.). Easy and clean enough for my taste.
Wilhelm ________________________________ Von: ImageJ Interest Group im Auftrag von Johannes Schindelin Gesendet: Mi 11.03.2009 22:08 An: [hidden email] Betreff: Re: Zooming new problem Hi, On Wed, 11 Mar 2009, Burger Wilhelm wrote: > as you mention, we have listed a number of different interpolation > methods in the source section of our website (imagingbook.com), > including cubic and other spline methods. I particularly recommend the > Catmull-Rom formulation for good results. I can also send you code for a > Lanczos interpolator, which has no visible advantage though. > > All these methods are pretty standard and implemented by stand-alone > code that could be copied directly into ImageProcessor's > getInterpolatedPixel() method and selected using a suitable mode switch. Usually I would not say anything, but since we discussed clean design earlier: I think it would not be appropriate to put this method into ImageProcessor (think MVC), at least not with a global switch as to which interpolation method is actually used. Ciao, Dscho |
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