Stitching image stacks
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Hello everyone,
This is my first time posting I hope my question will be very clear and someone will help me. I am working on images stacks 512x512 each image (dicom format). I need to stitch relative images (1st from stack A with 1st on stack B) and obtain an image 1024x1024. Basically aligned each correspondent image horizontally and eventually save the stitched stack as an image sequence. Any suggestions, I have tried to use TurboReg but the output is not what I am after. Thanks to all, Antonia. Antonia Lavorato | Principal Physicist| Medical Physics Department | Bupa Cromwell Hospital, Cromwell Road, London, SW5 0TU T: 0207 460 5619| F: 0207 460 5622| E: E: [hidden email] <mailto:[hidden email]> ________________________________________________________________________ Privileged or Confidential Information may be contained in this message. If you are not the addressee, you may not review or copy it, use information contained within it, nor deliver to anyone else. In such a case, you should destroy this message and kindly notify the sender. Bupa Cromwell Hospital does not accept legal responsibility for the contents of this message. Additionally, it does not accept responsibility for any damage caused by viruses being passed. Opinions, conclusions and other information in this message that do not relate to the official business of the Bupa Cromwell Hospital, are neither given nor endorsed by it. Thank you Bupa Cromwell Hospital is the business name of Medical Services International Ltd. Incorporated in London No. 1416977. Registered office: Cromwell Road, London SW5 0TU. ________________________________________________________________________ |
Re: Stitching image stacks
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What you're looking for is the plugin "stack combiner"
It's in the stack section of the imageJ plugins. -Will Ashby Vanderbilt University On Nov 18, 2009, at 5:03 AM, Antonia Lavorato wrote: > Hello everyone, > This is my first time posting I hope my question will be very clear and > someone will help me. > I am working on images stacks 512x512 each image (dicom format). I need > to stitch relative images (1st from stack A with 1st on stack B) and > obtain an image 1024x1024. Basically aligned each correspondent image > horizontally and eventually save the stitched stack as an image > sequence. > Any suggestions, I have tried to use TurboReg but the output is not what > I am after. > Thanks to all, Antonia. > > Antonia Lavorato | Principal Physicist| Medical Physics Department | > Bupa Cromwell Hospital, Cromwell Road, London, SW5 0TU > T: 0207 460 5619| F: 0207 460 5622| E: E: > [hidden email] > <mailto:[hidden email]> > > > > ________________________________________________________________________ > Privileged or Confidential Information may be contained in this message. If you are not the addressee, you may not review or copy it, use information contained within it, nor deliver to anyone else. In such a case, you should destroy this message and kindly notify the sender. > > Bupa Cromwell Hospital does not accept legal responsibility for the contents of this message. Additionally, it does not accept responsibility for any damage caused by viruses being passed. Opinions, conclusions and other information in this message that do not relate to the official business of the Bupa Cromwell Hospital, are neither given nor endorsed by it. Thank you > > Bupa Cromwell Hospital is the business name of Medical Services International Ltd. Incorporated in London No. 1416977. Registered office: Cromwell Road, London SW5 0TU. > ________________________________________________________________________ |
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Thanks, but I need to overlap part of the image too.
Any other suggestions? Maybe a combination of plugins? Antonia. -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Ashby, William Joseph Sent: November 18, 2009 11:37 AM To: [hidden email] Subject: Re: Stitching image stacks What you're looking for is the plugin "stack combiner" It's in the stack section of the imageJ plugins. -Will Ashby Vanderbilt University On Nov 18, 2009, at 5:03 AM, Antonia Lavorato wrote: > Hello everyone, > This is my first time posting I hope my question will be very clear and > someone will help me. > I am working on images stacks 512x512 each image (dicom format). I need > to stitch relative images (1st from stack A with 1st on stack B) and > obtain an image 1024x1024. Basically aligned each correspondent image > horizontally and eventually save the stitched stack as an image > sequence. > Any suggestions, I have tried to use TurboReg but the output is not what > I am after. > Thanks to all, Antonia. > > Antonia Lavorato | Principal Physicist| Medical Physics Department | > Bupa Cromwell Hospital, Cromwell Road, London, SW5 0TU > T: 0207 460 5619| F: 0207 460 5622| E: E: > [hidden email] > <mailto:[hidden email]> > > > > > Privileged or Confidential Information may be contained in this message. If you are not the addressee, you may not review or copy it, use information contained within it, nor deliver to anyone else. In such a case, you should destroy this message and kindly notify the sender. > > Bupa Cromwell Hospital does not accept legal responsibility for the contents of this message. Additionally, it does not accept responsibility for any damage caused by viruses being passed. Opinions, conclusions and other information in this message that do not relate to the official business of the Bupa Cromwell Hospital, are neither given nor endorsed by it. Thank you > > Bupa Cromwell Hospital is the business name of Medical Services International Ltd. Incorporated in London No. 1416977. Registered office: Cromwell Road, London SW5 0TU. > ________________________________________________________________________ ________________________________________________________________________ This e-mail has been scanned for all viruses by Star. The service is powered by MessageLabs. For more information on a proactive anti-virus service working around the clock, around the globe, visit: http://www.star.net.uk ________________________________________________________________________ ________________________________________________________________________ Privileged or Confidential Information may be contained in this message. If you are not the addressee, you may not review or copy it, use information contained within it, nor deliver to anyone else. In such a case, you should destroy this message and kindly notify the sender. Bupa Cromwell Hospital does not accept legal responsibility for the contents of this message. Additionally, it does not accept responsibility for any damage caused by viruses being passed. Opinions, conclusions and other information in this message that do not relate to the official business of the Bupa Cromwell Hospital, are neither given nor endorsed by it. Thank you Bupa Cromwell Hospital is the business name of Medical Services International Ltd. Incorporated in London No. 1416977. Registered office: Cromwell Road, London SW5 0TU. ________________________________________________________________________ |
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Hi,
I think you need to try TrakEM2 http://www.ini.uzh.ch/~acardona/trakem2.html Definitely you can do what you describe. Enjoy!, Marta Rivera-Alba Instituto Cajal. CSIC. Madrid. Spain On Wed, Nov 18, 2009 at 12:52 PM, Antonia Lavorato < [hidden email]> wrote: > Thanks, but I need to overlap part of the image too. > Any other suggestions? > Maybe a combination of plugins? > Antonia. > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Ashby, William Joseph > Sent: November 18, 2009 11:37 AM > To: [hidden email] > Subject: Re: Stitching image stacks > > What you're looking for is the plugin "stack combiner" > > It's in the stack section of the imageJ plugins. > > -Will Ashby > Vanderbilt University > > On Nov 18, 2009, at 5:03 AM, Antonia Lavorato wrote: > > > Hello everyone, > > This is my first time posting I hope my question will be very clear > and > > someone will help me. > > I am working on images stacks 512x512 each image (dicom format). I > need > > to stitch relative images (1st from stack A with 1st on stack B) and > > obtain an image 1024x1024. Basically aligned each correspondent image > > horizontally and eventually save the stitched stack as an image > > sequence. > > Any suggestions, I have tried to use TurboReg but the output is not > what > > I am after. > > Thanks to all, Antonia. > > > > Antonia Lavorato | Principal Physicist| Medical Physics Department | > > Bupa Cromwell Hospital, Cromwell Road, London, SW5 0TU > > T: 0207 460 5619| F: 0207 460 5622| E: E: > > [hidden email] > > <mailto:[hidden email]> > > > > > > > > > ________________________________________________________________________ > > Privileged or Confidential Information may be contained in this > message. If you are not the addressee, you may not review or copy it, > use information contained within it, nor deliver to anyone else. In > such a case, you should destroy this message and kindly notify the > sender. > > > > Bupa Cromwell Hospital does not accept legal responsibility for the > contents of this message. Additionally, it does not accept > responsibility for any damage caused by viruses being passed. Opinions, > conclusions and other information in this message that do not relate to > the official business of the Bupa Cromwell Hospital, are neither given > nor endorsed by it. Thank you > > > > Bupa Cromwell Hospital is the business name of Medical Services > International Ltd. Incorporated in London No. 1416977. Registered > office: Cromwell Road, London SW5 0TU. > > > ________________________________________________________________________ > > ________________________________________________________________________ > This e-mail has been scanned for all viruses by Star. The > service is powered by MessageLabs. For more information on a proactive > anti-virus service working around the clock, around the globe, visit: > http://www.star.net.uk > ________________________________________________________________________ > > ________________________________________________________________________ > Privileged or Confidential Information may be contained in this message. > If you are not the addressee, you may not review or copy it, use > information contained within it, nor deliver to anyone else. In such a > case, you should destroy this message and kindly notify the sender. > > Bupa Cromwell Hospital does not accept legal responsibility for the > contents of this message. Additionally, it does not accept responsibility > for any damage caused by viruses being passed. Opinions, conclusions and > other information in this message that do not relate to the official > business of the Bupa Cromwell Hospital, are neither given nor endorsed by > it. Thank you > > Bupa Cromwell Hospital is the business name of Medical Services > International Ltd. Incorporated in London No. 1416977. Registered office: > Cromwell Road, London SW5 0TU. > ________________________________________________________________________ > |
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Hi,
You may prefer to use 2D Stitching by Stephen Preibisch : http://fly.mpi-cbg.de/~preibisch/software.html or Mosaicj by Philippe Thevenaz : http://bigwww.epfl.ch/thevenaz/mosaicj/ Thomas Marta Rivera-Alba a écrit : > Hi, > > I think you need to try TrakEM2 > > http://www.ini.uzh.ch/~acardona/trakem2.html > > Definitely you can do what you describe. > > Enjoy!, > > Marta Rivera-Alba > > Instituto Cajal. CSIC. > Madrid. Spain > > On Wed, Nov 18, 2009 at 12:52 PM, Antonia Lavorato < > [hidden email]> wrote: > >> Thanks, but I need to overlap part of the image too. >> Any other suggestions? >> Maybe a combination of plugins? >> Antonia. >> >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >> Ashby, William Joseph >> Sent: November 18, 2009 11:37 AM >> To: [hidden email] >> Subject: Re: Stitching image stacks >> >> What you're looking for is the plugin "stack combiner" >> >> It's in the stack section of the imageJ plugins. >> >> -Will Ashby >> Vanderbilt University >> >> On Nov 18, 2009, at 5:03 AM, Antonia Lavorato wrote: >> >>> Hello everyone, >>> This is my first time posting I hope my question will be very clear >> and >>> someone will help me. >>> I am working on images stacks 512x512 each image (dicom format). I >> need >>> to stitch relative images (1st from stack A with 1st on stack B) and >>> obtain an image 1024x1024. Basically aligned each correspondent image >>> horizontally and eventually save the stitched stack as an image >>> sequence. >>> Any suggestions, I have tried to use TurboReg but the output is not >> what >>> I am after. >>> Thanks to all, Antonia. >>> >>> Antonia Lavorato | Principal Physicist| Medical Physics Department | >>> Bupa Cromwell Hospital, Cromwell Road, London, SW5 0TU >>> T: 0207 460 5619| F: 0207 460 5622| E: E: >>> [hidden email] >>> <mailto:[hidden email]> >>> >>> >>> >>> >> ________________________________________________________________________ >>> Privileged or Confidential Information may be contained in this >> message. If you are not the addressee, you may not review or copy it, >> use information contained within it, nor deliver to anyone else. In >> such a case, you should destroy this message and kindly notify the >> sender. >>> Bupa Cromwell Hospital does not accept legal responsibility for the >> contents of this message. Additionally, it does not accept >> responsibility for any damage caused by viruses being passed. Opinions, >> conclusions and other information in this message that do not relate to >> the official business of the Bupa Cromwell Hospital, are neither given >> nor endorsed by it. Thank you >>> Bupa Cromwell Hospital is the business name of Medical Services >> International Ltd. Incorporated in London No. 1416977. Registered >> office: Cromwell Road, London SW5 0TU. >> ________________________________________________________________________ >> >> ________________________________________________________________________ >> This e-mail has been scanned for all viruses by Star. The >> service is powered by MessageLabs. For more information on a proactive >> anti-virus service working around the clock, around the globe, visit: >> http://www.star.net.uk >> ________________________________________________________________________ >> >> ________________________________________________________________________ >> Privileged or Confidential Information may be contained in this message. >> If you are not the addressee, you may not review or copy it, use >> information contained within it, nor deliver to anyone else. In such a >> case, you should destroy this message and kindly notify the sender. >> >> Bupa Cromwell Hospital does not accept legal responsibility for the >> contents of this message. Additionally, it does not accept responsibility >> for any damage caused by viruses being passed. Opinions, conclusions and >> other information in this message that do not relate to the official >> business of the Bupa Cromwell Hospital, are neither given nor endorsed by >> it. Thank you >> >> Bupa Cromwell Hospital is the business name of Medical Services >> International Ltd. Incorporated in London No. 1416977. Registered office: >> Cromwell Road, London SW5 0TU. >> ________________________________________________________________________ >> > > -- /**********************************************************/ Thomas Boudier, MCU Université Pierre et Marie Curie, IFR 83. Bat B 7ème étage, porte 706D, Jussieu. Tel : 01 44 27 50 23 Fax : 01 44 27 22 91 /*******************************************************/ |
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