"compressed sensing again"
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Well as my test worked...
I just wanted to know if there are projects about compressed sensing and PALM imaging ? Thank you, Fabrice. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Fabrice,
what do you expect from "compressed sensing" with regard to scientific image processing and evaluation? Presently, I see little to no need for it. _______________________ For those not familiar with "compressed sensing" I should like to recommend as an "entry point" the publication: Hayes B. (2009) The best bits. American Scientist 97: 276-280. That can be downloaded for free from <http://bit-player.org/pubs> ________________________ Best Herbie On 11.09.12 18:04, fabrice senger wrote: > Well as my test worked... > > I just wanted to know if there are projects about compressed sensing > and PALM imaging ? > > Thank you, > > Fabrice. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi,
I'm by no mean a specialist (I'm not even sure I have understood correctly what compressed sensing is), but there have been at least two published papers that relate to compressed sensing in fluorescence microscopy: For speeding up imaging and putting less light to the sample: Compressive fluorescence microscopy for biological and hyperspectral imaging. Studer V, Bobin J, Chahid M, Mousavi HS, Candes E, Dahan M. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1679-87. Epub 2012 Jun 11. http://www.ncbi.nlm.nih.gov/pubmed/22689950 For speeding up pointillist super-resolution microscopy: Faster STORM using compressed sensing. Zhu L, Zhang W, Elnatan D, Huang B. Nat Methods. 2012 Apr 22;9(7):721-3. doi: 10.1038/nmeth.1978. Both papers did not use ImageJ for the image processing, so I guess Fabrice's wants to know if such approaches have been implemented or tried using ImageJ? Cheers, Christophe On Tue, Sep 11, 2012 at 7:33 PM, Herbie <[hidden email]> wrote: > Fabrice, > > what do you expect from "compressed sensing" with regard to scientific > image processing and evaluation? > > Presently, I see little to no need for it. > > _______________________ > > For those not familiar with "compressed sensing" I should like to > recommend as an "entry point" the publication: > > Hayes B. (2009) The best bits. American Scientist 97: 276-280. > > That can be downloaded for free from > > <http://bit-player.org/pubs> > ________________________ > > Best > > Herbie > > > > On 11.09.12 18:04, fabrice senger wrote: > >> Well as my test worked... >> >> I just wanted to know if there are projects about compressed sensing >> and PALM imaging ? >> >> Thank you, >> >> Fabrice. >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >> >> > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi all,
Given Fabrice's original e-mail, he is obviously more interested in the super-resolution approach. I have looked into it briefly, and the major limitation is the convex optimization library. After looking around, I think that JOptimizer is the best java offering, but given my limited knowledge of this very specialized field, it is not clear how one would implement an L2 norm constraint in this package as Zhu et al require. If anyone on the list has experience with JOptimizer (or a c open source convex optimization library) and can suggest how this would be done, I am more than happy to try to code a compressed sensing plugin. Jay Unruh, Research Advisor Stowers Institute for Medical Research -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christophe Leterrier Sent: Tuesday, September 11, 2012 3:18 PM To: [hidden email] Subject: Re: "compressed sensing again" Hi, I'm by no mean a specialist (I'm not even sure I have understood correctly what compressed sensing is), but there have been at least two published papers that relate to compressed sensing in fluorescence microscopy: For speeding up imaging and putting less light to the sample: Compressive fluorescence microscopy for biological and hyperspectral imaging. Studer V, Bobin J, Chahid M, Mousavi HS, Candes E, Dahan M. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1679-87. Epub 2012 Jun 11. http://www.ncbi.nlm.nih.gov/pubmed/22689950 For speeding up pointillist super-resolution microscopy: Faster STORM using compressed sensing. Zhu L, Zhang W, Elnatan D, Huang B. Nat Methods. 2012 Apr 22;9(7):721-3. doi: 10.1038/nmeth.1978. Both papers did not use ImageJ for the image processing, so I guess Fabrice's wants to know if such approaches have been implemented or tried using ImageJ? Cheers, Christophe On Tue, Sep 11, 2012 at 7:33 PM, Herbie <[hidden email]> wrote: > Fabrice, > > what do you expect from "compressed sensing" with regard to scientific > image processing and evaluation? > > Presently, I see little to no need for it. > > _______________________ > > For those not familiar with "compressed sensing" I should like to > recommend as an "entry point" the publication: > > Hayes B. (2009) The best bits. American Scientist 97: 276-280. > > That can be downloaded for free from > > <http://bit-player.org/pubs> > ________________________ > > Best > > Herbie > > > > On 11.09.12 18:04, fabrice senger wrote: > >> Well as my test worked... >> >> I just wanted to know if there are projects about compressed sensing >> and PALM imaging ? >> >> Thank you, >> >> Fabrice. >> >> -- >> ImageJ mailing list: >> http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.ht >> ml> >> >> > -- > ImageJ mailing list: > http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.htm > l> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: "compressed sensing again"
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Hello,
Christophe is right. I do not plan to develop something like that, as I would not be able to do it. It sounds very interesting, tools are allready available, especially the code from Zhu et al. As I noticed that in the list some people are interested in super resolution, spot detection and image reconstruction I thought it would of interest to start such a topic. All the best, Fabrice. 2012/9/12 Unruh, Jay <[hidden email]> > Hi all, > > Given Fabrice's original e-mail, he is obviously more interested in the > super-resolution approach. I have looked into it briefly, and the major > limitation is the convex optimization library. After looking around, I > think that JOptimizer is the best java offering, but given my limited > knowledge of this very specialized field, it is not clear how one would > implement an L2 norm constraint in this package as Zhu et al require. If > anyone on the list has experience with JOptimizer (or a c open source > convex optimization library) and can suggest how this would be done, I am > more than happy to try to code a compressed sensing plugin. > > Jay Unruh, > Research Advisor > Stowers Institute for Medical Research > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Christophe Leterrier > Sent: Tuesday, September 11, 2012 3:18 PM > To: [hidden email] > Subject: Re: "compressed sensing again" > > Hi, > > I'm by no mean a specialist (I'm not even sure I have understood correctly > what compressed sensing is), but there have been at least two published > papers that relate to compressed sensing in fluorescence microscopy: > > For speeding up imaging and putting less light to the sample: > Compressive fluorescence microscopy for biological and hyperspectral > imaging. > Studer V, Bobin J, Chahid M, Mousavi HS, Candes E, Dahan M. > Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1679-87. Epub 2012 Jun 11. > http://www.ncbi.nlm.nih.gov/pubmed/22689950 > > For speeding up pointillist super-resolution microscopy: > Faster STORM using compressed sensing. > Zhu L, Zhang W, Elnatan D, Huang B. > Nat Methods. 2012 Apr 22;9(7):721-3. doi: 10.1038/nmeth.1978. > > Both papers did not use ImageJ for the image processing, so I guess > Fabrice's wants to know if such approaches have been implemented or tried > using ImageJ? > > Cheers, > > Christophe > > On Tue, Sep 11, 2012 at 7:33 PM, Herbie <[hidden email]> wrote: > > > Fabrice, > > > > what do you expect from "compressed sensing" with regard to scientific > > image processing and evaluation? > > > > Presently, I see little to no need for it. > > > > _______________________ > > > > For those not familiar with "compressed sensing" I should like to > > recommend as an "entry point" the publication: > > > > Hayes B. (2009) The best bits. American Scientist 97: 276-280. > > > > That can be downloaded for free from > > > > <http://bit-player.org/pubs> > > ________________________ > > > > Best > > > > Herbie > > > > > > > > On 11.09.12 18:04, fabrice senger wrote: > > > >> Well as my test worked... > >> > >> I just wanted to know if there are projects about compressed sensing > >> and PALM imaging ? > >> > >> Thank you, > >> > >> Fabrice. > >> > >> -- > >> ImageJ mailing list: > >> http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.ht > >> ml> > >> > >> > > -- > > ImageJ mailing list: > > http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.htm > > l> > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thanks for writing!
For clarification: "Compressed sensing", as the name and the addressed examples imply, is a technique for data/image-acquisition. ImageJ is a tool-set for image processing and evaluation. Of course, both fields have some overlap. Whether it's worthwhile to enter the field of some rather special application of "compressed sensing" with ImageJ-plugins appears questionable to me at least with respect to the profit/effort-ratio. Presently, it seems like writing code for image reconstruction from an image acquisition apparatus that exists in a single laboratory, although one should expect that such an apparatus delivers images not raw data, i.e. it contains a proper reconstruction program. I hope the above clarifies my previous statement. Best Herbie _______________________________________ On 12.09.12 09:01, fabrice senger wrote: > Hello, > > Christophe is right. > I do not plan to develop something like that, as I would not be able to do > it. > It sounds very interesting, tools are allready available, especially the > code from Zhu et al. > > As I noticed that in the list some people are interested in super > resolution, spot detection and image reconstruction I thought it would of > interest to start such a topic. > > All the best, > > Fabrice. > > 2012/9/12 Unruh, Jay<[hidden email]> > >> Hi all, >> >> Given Fabrice's original e-mail, he is obviously more interested in the >> super-resolution approach. I have looked into it briefly, and the major >> limitation is the convex optimization library. After looking around, I >> think that JOptimizer is the best java offering, but given my limited >> knowledge of this very specialized field, it is not clear how one would >> implement an L2 norm constraint in this package as Zhu et al require. If >> anyone on the list has experience with JOptimizer (or a c open source >> convex optimization library) and can suggest how this would be done, I am >> more than happy to try to code a compressed sensing plugin. >> >> Jay Unruh, >> Research Advisor >> Stowers Institute for Medical Research >> >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >> Christophe Leterrier >> Sent: Tuesday, September 11, 2012 3:18 PM >> To: [hidden email] >> Subject: Re: "compressed sensing again" >> >> Hi, >> >> I'm by no mean a specialist (I'm not even sure I have understood correctly >> what compressed sensing is), but there have been at least two published >> papers that relate to compressed sensing in fluorescence microscopy: >> >> For speeding up imaging and putting less light to the sample: >> Compressive fluorescence microscopy for biological and hyperspectral >> imaging. >> Studer V, Bobin J, Chahid M, Mousavi HS, Candes E, Dahan M. >> Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1679-87. Epub 2012 Jun 11. >> http://www.ncbi.nlm.nih.gov/pubmed/22689950 >> >> For speeding up pointillist super-resolution microscopy: >> Faster STORM using compressed sensing. >> Zhu L, Zhang W, Elnatan D, Huang B. >> Nat Methods. 2012 Apr 22;9(7):721-3. doi: 10.1038/nmeth.1978. >> >> Both papers did not use ImageJ for the image processing, so I guess >> Fabrice's wants to know if such approaches have been implemented or tried >> using ImageJ? >> >> Cheers, >> >> Christophe >> >> On Tue, Sep 11, 2012 at 7:33 PM, Herbie<[hidden email]> wrote: >> >>> Fabrice, >>> >>> what do you expect from "compressed sensing" with regard to scientific >>> image processing and evaluation? >>> >>> Presently, I see little to no need for it. >>> >>> _______________________ >>> >>> For those not familiar with "compressed sensing" I should like to >>> recommend as an "entry point" the publication: >>> >>> Hayes B. (2009) The best bits. American Scientist 97: 276-280. >>> >>> That can be downloaded for free from >>> >>> <http://bit-player.org/pubs> >>> ________________________ >>> >>> Best >>> >>> Herbie >>> >>> >>> >>> On 11.09.12 18:04, fabrice senger wrote: >>> >>>> Well as my test worked... >>>> >>>> I just wanted to know if there are projects about compressed sensing >>>> and PALM imaging ? >>>> >>>> Thank you, >>>> >>>> Fabrice. >>>> >>>> -- >>>> ImageJ mailing list: >>>> http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.ht >>>> ml> >>>> >>>> >>> -- >>> ImageJ mailing list: >>> http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.htm >>> l> >>> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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