3D reconstruction of volume
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We are trying to make volume projections of some confocal z slices
through a cell. There is cytoplasmic label and some concentrated membrane labeling. There are also large vacuoles and the nucleus where there is no label. Is there any way to get those black holes in the cytoplasm to show up as defined structures in the projections? They are obscured by the cytoplasmic label in a standard projection because they are of much lower intensity. If you try to project just hte lower intensity values, they are obscured by the fact that the extracellular background is equally black. Any ideas? Thanks- Dave Dr. David Knecht Department of Molecular and Cell Biology Co-head Flow Cytometry and Confocal Microscopy Facility U-3125 91 N. Eagleville Rd. University of Connecticut Storrs, CT 06269 860-486-2200 860-486-4331 (fax) |
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David,
You could draw a ROI ( wedge) from the interior outward and clear the ROI (option to do so for entire stack). This way it looks like a cut pie upon 3D projection. You could play with opacity and surface/interior weights to emphasize the inner features, though I've not had great success this way. You should also try the Volume Viewer/3D Slicer and/or VolumeJ plugins that can perform this type of rendering option (ROI not required). Animating a series of XZ or YZ reslice projections would show what you want to show, too. David Knecht-charter wrote: > We are trying to make volume projections of some confocal z slices > through a cell. There is cytoplasmic label and some concentrated > membrane labeling. There are also large vacuoles and the nucleus > where there is no label. Is there any way to get those black holes in > the cytoplasm to show up as defined structures in the projections? > They are obscured by the cytoplasmic label in a standard projection > because they are of much lower intensity. If you try to project just > hte lower intensity values, they are obscured by the fact that the > extracellular background is equally black. Any ideas? Thanks- Dave > > > Dr. David Knecht > Department of Molecular and Cell Biology > Co-head Flow Cytometry and Confocal Microscopy Facility > U-3125 > 91 N. Eagleville Rd. > University of Connecticut > Storrs, CT 06269 > 860-486-2200 > 860-486-4331 (fax) -- __ Vytas Bindokas, Ph.D. Research Assoc. / Assoc. Prof., Director, BSD Light Microscopy Core Facility Dept Neurobiol Pharmacol Physiol MC0926 947 E 58th Street The University of Chicago Chicago IL 60637 Room Abbott 120 773-702-4875 email [hidden email] web site for LMCF: http://digital.bsd.uchicago.edu/index.html This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. |
shot in the dark: image library for freepascal/xcode?
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hi,
apologies if this is off-target, but i am floundering for resources and hope someone in the audience might be able to help. i am trying to simulate 2D diffusion under a variety of circumstances: flow, transient binding, etc. the code is actually quite simple and was built on the FPC carbon application which comes as part of the xcode integration kit for freepascal. the problem for me is trying to generate image snapshots (tiff, jpeg, png, whatever, i dont care!) of the state of my diffusion simulation at different time points. i did something similar using codewarrior pascal ages ago (no idea where that code went, but would have been system 9), and recall that it was not trivial even using the metroworks libraries. also did something similar using the original (pascal based) nih image. that was great because image took care of all the file-writing work. i know, i know. i should learn java. for now the question is: can anyone refer me to a library for free pascal (running on os x 10.4 under xcode) which will simplify writing an image file format? suggestions would also be welcome if there is an alternate version of (preferably mac based) pascal for which the libraries exist. i can also work with windows if need be. thanks very much in advance, kurt . ------------------------------------------------------------ Dr. Kurt I. Anderson Beatson Institute for Cancer Research Garscube Estate,Switchback Road Glasgow, G61 1BD Scotland United Kingdom [hidden email] t: +44 141 330 2864 f: +44 141 942 6521 |
Re: 3D reconstruction of volume
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In reply to this post by Knecht, David
Hi David,
You may just want to show a single slice from the stack showing the section of the cell with holes and also show an 'axial' section through it (draw line; Menu:image>stacks>reslice). Something like this: http://www.macbiophotonics.ca/images/axialsection.jpg (CAAX-GFP and SNARF). Best, Tony Tony J. Collins, Ph.D. McMaster Biophotonics Facility Dept. Biochemistry and Biomedical Sciences HSC 4H21A McMaster University, Hamilton, ON, L8N 3Z5 (905) 525 9140 x28812(off.)/x26488(lab) [hidden email] www.macbiophotonics.ca > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > David Knecht-charter > Sent: October 24, 2007 11:47 PM > To: [hidden email] > Subject: 3D reconstruction of volume > > We are trying to make volume projections of some confocal z slices > through a cell. There is cytoplasmic label and some concentrated > membrane labeling. There are also large vacuoles and the nucleus > where there is no label. Is there any way to get those black holes > in the cytoplasm to show up as defined structures in the > projections? They are obscured by the cytoplasmic label in a > standard projection because they are of much lower intensity. If you > try to project just hte lower intensity values, they are obscured by > the fact that the extracellular background is equally black. Any > ideas? Thanks- Dave > > > Dr. David Knecht > Department of Molecular and Cell Biology > Co-head Flow Cytometry and Confocal Microscopy Facility > U-3125 > 91 N. Eagleville Rd. > University of Connecticut > Storrs, CT 06269 > 860-486-2200 > 860-486-4331 (fax) |
Re: 3D reconstruction of volume
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In reply to this post by vbindokas
David,
Here's another idea. What would happen if you invert the images? That is, use Edit>Invert to convert the dark pixels to light ones, and vice versa. You could then reconstruct that volume, in which the nuclei would dominate, and merge it with one from the original images. I have done something like this with brightfield images of H&E stained tissue. You can see an example on our department's home page: www.temple.edu/biology. Joel Date sent: Thu, 25 Oct 2007 06:56:38 -0500 Send reply to: ImageJ Interest Group <[hidden email]> From: vbindoka <[hidden email]> Subject: Re: 3D reconstruction of volume To: [hidden email] > David, > You could draw a ROI ( wedge) from the interior outward and clear the > ROI (option to do so for entire stack). This way it looks like a cut pie > upon 3D projection. You could play with opacity and surface/interior > weights to emphasize the inner features, though I've not had great > success this way. You should also try the Volume Viewer/3D Slicer and/or > VolumeJ plugins that can perform this type of rendering option (ROI not > required). Animating a series of XZ or YZ reslice projections would show > what you want to show, too. > > > David Knecht-charter wrote: > > We are trying to make volume projections of some confocal z slices > > through a cell. There is cytoplasmic label and some concentrated > > membrane labeling. There are also large vacuoles and the nucleus > > where there is no label. Is there any way to get those black holes in > > the cytoplasm to show up as defined structures in the projections? > > They are obscured by the cytoplasmic label in a standard projection > > because they are of much lower intensity. If you try to project just > > hte lower intensity values, they are obscured by the fact that the > > extracellular background is equally black. Any ideas? Thanks- Dave > > > > > > Dr. David Knecht > > Department of Molecular and Cell Biology > > Co-head Flow Cytometry and Confocal Microscopy Facility > > U-3125 > > 91 N. Eagleville Rd. > > University of Connecticut > > Storrs, CT 06269 > > 860-486-2200 > > 860-486-4331 (fax) > > -- > __ > > Vytas Bindokas, Ph.D. > Research Assoc. / Assoc. Prof., > Director, BSD Light Microscopy Core Facility > Dept Neurobiol Pharmacol Physiol MC0926 > 947 E 58th Street > The University of Chicago > Chicago IL 60637 > Room Abbott 120 > 773-702-4875 > > email [hidden email] > web site for LMCF: > http://digital.bsd.uchicago.edu/index.html > > > > This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. 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 |
Re: shot in the dark: image library for freepascal/xcode?
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In reply to this post by Kurt Anderson-3
> the problem for me is trying to generate image snapshots (tiff, jpeg,
> png, whatever, i dont care!) of the state of my diffusion simulation at > different time points. Why not write images in portable pixmap format: http://en.wikipedia.org/wiki/Netpbm_format This needs only some PRINT statement in your favorite language, and is *very easy* to figure out and implement (no need to install anything in particular). ImageJ reads PPM-files out of the box (like all other image processing/editing software, e.g. GIMP). Or use ImageMagick or similar to convert to PNG/JPEG/TIFF/... Just to give a quick impression of how simple and intuitive this format is, here is an example of a small graymap (try to copy/paste & save this using your favorite text editor, and open it using ImageJ): -------------------- cut here ----------------------- P2 # feep.pgm 24 7 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 3 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 15 15 15 0 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 15 0 0 3 3 3 0 0 0 7 7 7 0 0 0 11 11 11 0 0 0 15 15 15 15 0 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 0 0 0 3 0 0 0 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -------------------- cut here ----------------------- regards, Adrian |
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In reply to this post by vbindokas
I am running ImageJ 1.38 on Mac OS X (10.4.10), having
a memory setting problem. When I tried to allocate more memory by going to Edit / Options / Memory&Threads.. The dialog appears, but when I type in a larger memory size and click OK, a warning appears.. "imagej is unable to change memory limit. For more information refer to the installation notes" I've found a similar problem discussed on the LIST ARCHIVE but I couldn't understand it well. >> To set the memory limit using Edit>Options>Memory you need to be >>running the Mac OS X application or the Windows application >>(ImageJ.exe), and you must have downloaded the full 1.32 or later >>distribution. Both applications use a microscope icon. You can set the >>limit using the -Xmx option if you run ImageJ from the command line or >>a script. As far as I know, there is no way to increase the memory >>limit when running ImageJ by double-clicking on ij.jar. I am not running imageJ from ij.jar. I am running the ImageJ program by double clicking ImageJ1.38.app icon. Does this also mean that I can't change the memory from Edit>Options>Memory &Threads...?? Naoki Irie |
Re: Mac OS X memory
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Naoki, even though i'm also new at this i've already had a similar problem.
i'm running imagej under windows and once you've setted the memory => Edit => Options => Memry & Threads, you have to restart the program so this change can take effect. note that there is a max memory limit (at least for windows) which i think is 2 Gb,so anything below this will not take effect. Pedro Hervé F. |
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In reply to this post by naoki irie
On Mac OS X, the Edit>Options>Memory & Threads command is not able to
change the memory allocation if the name of the ImageJ application has been changed. For example, it will not work if you change the name from "ImageJ" to "ImageJ1.38". -wayne On Oct 29, 2007, at 3:24 AM, Naoki Irie wrote: > I am running ImageJ 1.38 on Mac OS X (10.4.10), having > a memory setting problem. > > When I tried to allocate more memory by going to > Edit / Options / Memory&Threads.. > The dialog appears, but when I type in a larger memory size and > click OK, a warning appears.. > > "imagej is unable to change memory limit. For > more information refer to the installation notes" > > I've found a similar problem discussed on the LIST ARCHIVE > but I couldn't understand it well. > > >> To set the memory limit using Edit>Options>Memory you need to be > >>running the Mac OS X application or the Windows application > >>(ImageJ.exe), and you must have downloaded the full 1.32 or later > >>distribution. Both applications use a microscope icon. You can set > the > >>limit using the -Xmx option if you run ImageJ from the command line > or > >>a script. As far as I know, there is no way to increase the memory > >>limit when running ImageJ by double-clicking on ij.jar. > > I am not running imageJ from ij.jar. I am running the ImageJ program > by double clicking ImageJ1.38.app icon. > Does this also mean that I can't change the memory from > Edit>Options>Memory &Threads...?? > > Naoki Irie > |
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> On Mac OS X, the Edit>Options>Memory & Threads command is not able
> to change the memory allocation if the name of the ImageJ > application has been changed. For example, it will not work if you > change the name from "ImageJ" to "ImageJ1.38". Thank you. This was just the cause of my memory problem. Renaming the file name (ImageJ1.38.app) back to ImageJ.app solved the problem. Naoki Irie > -wayne > > On Oct 29, 2007, at 3:24 AM, Naoki Irie wrote: > >> I am running ImageJ 1.38 on Mac OS X (10.4.10), having >> a memory setting problem. >> >> When I tried to allocate more memory by going to >> Edit / Options / Memory&Threads.. >> The dialog appears, but when I type in a larger memory size and >> click OK, a warning appears.. >> >> "imagej is unable to change memory limit. For >> more information refer to the installation notes" >> >> I've found a similar problem discussed on the LIST ARCHIVE >> but I couldn't understand it well. >> >> >> To set the memory limit using Edit>Options>Memory you need to be >> >>running the Mac OS X application or the Windows application >> >>(ImageJ.exe), and you must have downloaded the full 1.32 or later >> >>distribution. Both applications use a microscope icon. You can >> set the >> >>limit using the -Xmx option if you run ImageJ from the command >> line or >> >>a script. As far as I know, there is no way to increase the memory >> >>limit when running ImageJ by double-clicking on ij.jar. >> >> I am not running imageJ from ij.jar. I am running the ImageJ program >> by double clicking ImageJ1.38.app icon. >> Does this also mean that I can't change the memory from >> Edit>Options>Memory &Threads...?? >> >> Naoki Irie >> > |
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