manual stitching problem
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Romin, Yevgeniy/Sloan Kettering Institute |
manual stitching problem
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear List I am currently having the following problem. I ran a timelapse using the Leica SP8 software, it was a 3x3 tilescan z-stack with 100 timeframes. There was a lot of cell movement in the timelapse, and the automatic stitching in the Leica software did not do a very good job of stitching the images together. All I need is to stitch together the maximum projection of the z-stack by manually aligning them. I have tried cropping the projection into it's respective 9 parts, both in Imaris and in LAS, since it is impossible to get the single tile files from the original lif file in the Leica software. Then I have tried stitching these in XUV stitch, but the software sees the timepoints in both *.lif and *.ims files that I cropped as z-planes instead of timepoints, so I am having difficulty stitching it together. XUV stitch seemed appropriate since I can manually align the stacks, something I can't do in Metamorph, for example. If anybody has came across a similar problem and knows the solution or has any suggestions, they will be greatly appreciated. Thanks to all of you in advance, Yevgeniy Romin ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** In image properties in Imarus you should be able to swap Z and T. -mc -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Yevgeniy Romin Sent: Monday, September 23, 2013 11:04 AM To: [hidden email] Subject: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear List I am currently having the following problem. I ran a timelapse using the Leica SP8 software, it was a 3x3 tilescan z-stack with 100 timeframes. There was a lot of cell movement in the timelapse, and the automatic stitching in the Leica software did not do a very good job of stitching the images together. All I need is to stitch together the maximum projection of the z-stack by manually aligning them. I have tried cropping the projection into it's respective 9 parts, both in Imaris and in LAS, since it is impossible to get the single tile files from the original lif file in the Leica software. Then I have tried stitching these in XUV stitch, but the software sees the timepoints in both *.lif and *.ims files that I cropped as z-planes instead of timepoints, so I am having difficulty stitching it together. XUV stitch seemed appropriate since I can manually align the stacks, something I can't do in Metamorph, for example. If anybody has came across a similar problem and knows the solution or has any suggestions, they will be greatly appreciated. Thanks to all of you in advance, Yevgeniy Romin ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Before you close the LAS software you safe the Lif file and you also want to safe the tiff images. Then you can create a stack of every single tile and later stitch all 9 tiles stacks or the projections of the stacks together. I case the LAS stitching is not good enough I usually use ImageJ. Steve -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael Sent: Monday, September 23, 2013 10:09 AM To: [hidden email] Subject: Re: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** In image properties in Imarus you should be able to swap Z and T. -mc -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Yevgeniy Romin Sent: Monday, September 23, 2013 11:04 AM To: [hidden email] Subject: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear List I am currently having the following problem. I ran a timelapse using the Leica SP8 software, it was a 3x3 tilescan z-stack with 100 timeframes. There was a lot of cell movement in the timelapse, and the automatic stitching in the Leica software did not do a very good job of stitching the images together. All I need is to stitch together the maximum projection of the z-stack by manually aligning them. I have tried cropping the projection into it's respective 9 parts, both in Imaris and in LAS, since it is impossible to get the single tile files from the original lif file in the Leica software. Then I have tried stitching these in XUV stitch, but the software sees the timepoints in both *.lif and *.ims files that I cropped as z-planes instead of timepoints, so I am having difficulty stitching it together. XUV stitch seemed appropriate since I can manually align the stacks, something I can't do in Metamorph, for example. If anybody has came across a similar problem and knows the solution or has any suggestions, they will be greatly appreciated. Thanks to all of you in advance, Yevgeniy Romin ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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Romin, Yevgeniy/Sloan Kettering Institute |
Re: manual stitching problem
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I thought about doing that, but thought that I may be able to avoid recreating each tile myself. Do you know if ImageJ will stitch together straight-up *.lif files? Which plugins do you recommend? Thanks in advance, Yevgeniy ________________________________________ From: Confocal Microscopy List [[hidden email]] on behalf of Alexander,Steve [[hidden email]] Sent: Monday, September 23, 2013 11:18 AM To: [hidden email] Subject: Re: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Before you close the LAS software you safe the Lif file and you also want to safe the tiff images. Then you can create a stack of every single tile and later stitch all 9 tiles stacks or the projections of the stacks together. I case the LAS stitching is not good enough I usually use ImageJ. Steve -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael Sent: Monday, September 23, 2013 10:09 AM To: [hidden email] Subject: Re: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** In image properties in Imarus you should be able to swap Z and T. -mc -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Yevgeniy Romin Sent: Monday, September 23, 2013 11:04 AM To: [hidden email] Subject: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear List I am currently having the following problem. I ran a timelapse using the Leica SP8 software, it was a 3x3 tilescan z-stack with 100 timeframes. There was a lot of cell movement in the timelapse, and the automatic stitching in the Leica software did not do a very good job of stitching the images together. All I need is to stitch together the maximum projection of the z-stack by manually aligning them. I have tried cropping the projection into it's respective 9 parts, both in Imaris and in LAS, since it is impossible to get the single tile files from the original lif file in the Leica software. Then I have tried stitching these in XUV stitch, but the software sees the timepoints in both *.lif and *.ims files that I cropped as z-planes instead of timepoints, so I am having difficulty stitching it together. XUV stitch seemed appropriate since I can manually align the stacks, something I can't do in Metamorph, for example. If anybody has came across a similar problem and knows the solution or has any suggestions, they will be greatly appreciated. Thanks to all of you in advance, Yevgeniy Romin ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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JOEL B. SHEFFIELD |
Re: manual stitching problem
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In reply to this post by mcammer
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** This may be too simple a solution, but if you are able to generate the Max projections of each tile, you might be able to stitch them together with Autostitch, a free program that works only on jpeg files, but has done some remarkable work with some of our images. Joel On Mon, Sep 23, 2013 at 11:09 AM, Cammer, Michael < [hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > In image properties in Imarus you should be able to swap Z and T. > -mc > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Yevgeniy Romin > Sent: Monday, September 23, 2013 11:04 AM > To: [hidden email] > Subject: manual stitching problem > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Dear List > > I am currently having the following problem. I ran a timelapse using the > Leica SP8 software, it was a 3x3 tilescan z-stack with 100 timeframes. > There was a lot of cell movement in the timelapse, and the automatic > stitching in the Leica software did not do a very good job of stitching the > images together. All I need is to stitch together the maximum projection > of the z-stack by manually aligning them. I have tried cropping the > projection into it's respective 9 parts, both in Imaris and in LAS, since > it is impossible to get the single tile files from the original lif file in > the Leica software. Then I have tried stitching these in XUV stitch, but > the software sees the timepoints in both *.lif and *.ims files that I > cropped as z-planes instead of timepoints, so I am having difficulty > stitching it together. XUV stitch seemed appropriate since I can manually > align the stacks, something I can't do in Metamorph, for example. > > If anybody has came across a similar problem and knows the solution or has > any suggestions, they will be greatly appreciated. > > Thanks to all of you in advance, > > Yevgeniy Romin > > ===================================================================== > > > > Please note that this e-mail and any files transmitted from > > Memorial Sloan-Kettering Cancer Center may be privileged, > confidential, > > and protected from disclosure under applicable law. If the reader of > > this message is not the intended recipient, or an employee or agent > > responsible for delivering this message to the intended recipient, > > you are hereby notified that any reading, dissemination, distribution, > > copying, or other use of this communication or any of its attachments > > is strictly prohibited. If you have received this communication in > > error, please notify the sender immediately by replying to this > message > > and deleting this message, any attachments, and all copies and backups > > from your computer. > -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
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Johannes Schindelin |
Re: manual stitching problem
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In reply to this post by Romin, Yevgeniy/Sloan Kettering Institute
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Yevgeniy, On Mon, 23 Sep 2013, Yevgeniy Romin wrote: > I thought about doing that, but thought that I may be able to avoid > recreating each tile myself. Do you know if ImageJ will stitch together > straight-up *.lif files? Which plugins do you recommend? The easiest way to install the most useful plugins for life sciences is to go with the Fiji distribution of ImageJ: http://fiji.sc/. (Although I am the maintainer of this software, I have no commercial benefit from it, so this is not a commercial response). Fiji includes an updater (which is actually the ImageJ2 updater) to keep you up-to-date without major hassles. Fiji includes Bio-Formats to open .lif files. There is even a way to follow the most recent Bio-Formats in case you need a recent bug fix that did not make it into a stable Bio-Formats release yet: http://fiji.sc/Bio-Formats#Daily_builds As to stitching, Fiji includes this plugin: http://fiji.sc/Stitching. I would be surprised if you could not make it do what you require... Ciao, Johannes |
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Johannes Schindelin |
Re: manual stitching problem
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In reply to this post by JOEL B. SHEFFIELD
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Joel, On Mon, 23 Sep 2013, JOEL B. SHEFFIELD wrote: > This may be too simple a solution, but if you are able to generate the > Max projections of each tile, you might be able to stitch them together > with Autostitch, a free program that works only on jpeg files, but has > done some remarkable work with some of our images. Please note that all .jpeg files are good for are pretty pictures. You cannot perform scientifically sound image analysis on them. Ciao, Johannes |
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Romin, Yevgeniy/Sloan Kettering Institute |
Re: manual stitching problem
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Thanks very much for all your inputs. Fiji seems to be the way to go, even though it's still not perfect, but definitely better then LAS was. I may still have to do some manual compiling from the *.tif files, but that's life I guess :) Thanks very much again, Yevgeniy ________________________________________ From: Confocal Microscopy List [[hidden email]] on behalf of Johannes Schindelin [[hidden email]] Sent: Monday, September 23, 2013 1:18 PM To: [hidden email] Subject: Re: manual stitching problem ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Joel, On Mon, 23 Sep 2013, JOEL B. SHEFFIELD wrote: > This may be too simple a solution, but if you are able to generate the > Max projections of each tile, you might be able to stitch them together > with Autostitch, a free program that works only on jpeg files, but has > done some remarkable work with some of our images. Please note that all .jpeg files are good for are pretty pictures. You cannot perform scientifically sound image analysis on them. Ciao, Johannes ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
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JOEL B. SHEFFIELD |
Re: manual stitching problem
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In reply to this post by Johannes Schindelin
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Johannes. Of course, and I made the point that the stitching worked only with jpegs. Nevertheless, if one is trying to generate a low magnification image without quantitation, this sort of program can be useful, If you are not familiar with it, it also does a fair amount of warping to make things fit. Again, useful for a general impression, but not even for quantitative measurement. On Mon, Sep 23, 2013 at 1:18 PM, Johannes Schindelin <[hidden email]>wrote: > Hi Joel, > > On Mon, 23 Sep 2013, JOEL B. SHEFFIELD wrote: > > > This may be too simple a solution, but if you are able to generate the > > Max projections of each tile, you might be able to stitch them together > > with Autostitch, a free program that works only on jpeg files, but has > > done some remarkable work with some of our images. > > Please note that all .jpeg files are good for are pretty pictures. You > cannot perform scientifically sound image analysis on them. > > Ciao, > Johannes > -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
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