# 3D projections

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## 3D projections

 I have a confocal data stack where the voxels are 0.06 x 0.06 x 0.5.  When Z projected at a 90° angle, you get a series of interdigitated white and black lines unless you interpolate.  I am curious as to why the data is represented this way.  If the sections are 0.5µm thick, and stacked upon each other, where is the black space between coming from?  I would have expected that looking from the side, you would see a white smear without a lot of surface depth cueing.  Thanks- Dave Dr. David Knecht Professor, Department of Molecular and Cell Biology University of Connecticut 91 N. Eagleville Rd. U-3125 Storrs, CT 06269-3125 860-486-2200 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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## Re: 3D projections

 This is just a guess, but I assume that ImageJ considers each slice to be essentially infinitely thin, spaced at the step distance. Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] Office:  Biolife 311 URL:  *https://bio.cst.temple.edu/~jbs/  * On Mon, Mar 30, 2020 at 3:53 PM Knecht, David <[hidden email]> wrote: > I have a confocal data stack where the voxels are 0.06 x 0.06 x 0.5.  When > Z projected at a 90° angle, you get a series of interdigitated white and > black lines unless you interpolate.  I am curious as to why the data is > represented this way.  If the sections are 0.5µm thick, and stacked upon > each other, where is the black space between coming from?  I would have > expected that looking from the side, you would see a white smear without a > lot of surface depth cueing.  Thanks- Dave > > Dr. David Knecht > Professor, Department of Molecular and Cell Biology > University of Connecticut > 91 N. Eagleville Rd. > U-3125 > Storrs, CT 06269-3125 > 860-486-2200 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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## Re: 3D projections

 This has always confused me.  After all, ImageJ does not treat PIXELS as infinitely small in x and y - so why should it consider  VOXELS to be infinitely thin in z (but with finite  width and height)? -- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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## Re: 3D projections

 I have seen systems, such as the Leica SP2 software. in which the contents of each slice is extended through its depth, but that makes the assumption that the section is uniform through its depth.  I wonder if that is valid. That is, does the image that is recorded include a full Z average of the psf? In the Leica, it makes the Z slice image very blocky. Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] Office:  Biolife 311 URL:  *https://bio.cst.temple.edu/~jbs/  * On Mon, Mar 30, 2020 at 5:49 PM Kenneth Sloan <[hidden email]> wrote: > This has always confused me.  After all, ImageJ does not treat PIXELS as > infinitely small in x and y - so why should it consider  VOXELS to be > infinitely thin in z (but with finite  width and height)? > > -- > Kenneth Sloan > [hidden email] > Vision is the art of seeing what is invisible to others. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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## Re: 3D projections

 In reply to this post by Kenneth Sloan-2 "ImageJ does not treat PIXELS as infinitely small in x and y [...]" If you would, which were correct, you wouldn't see anything. Therefore and in general, the cheapest interpolation is applied: Little squares or rectangles of constant value(s). Actually, such block images are incorrect as well, because the correct interpolation is a totally different one that is much more costly and cannot be realized by common display technology. Regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 30.03.20 um 23:49 schrieb Kenneth Sloan: > This has always confused me.  After all, ImageJ does not treat PIXELS as infinitely small in x and y - so why should it consider  VOXELS to be infinitely thin in z (but with finite  width and height)? > > -- > Kenneth Sloan > [hidden email] > Vision is the art of seeing what is invisible to others. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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## Re: 3D projections

 Understood.  Now...why doesn't the same logic apply to image "planes"? -- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. Begin forwarded message: > From: Herbie <[hidden email]> > Subject: Re: 3D projections > Date: March 31, 2020 at 05:37:15 CDT > To: [hidden email] > Reply-To: [hidden email] > > "ImageJ does not treat PIXELS as infinitely small in x and y [...]" > > If you would, which were correct, you wouldn't see anything. > Therefore and in general, the cheapest interpolation is applied: > Little squares or rectangles of constant value(s). > Actually, such block images are incorrect as well, because the correct interpolation is a totally different one that is much more costly and cannot be realized by common display technology. > > Regards > > Herbie > > ::::::::::::::::::::::::::::::::::::::::::: > Am 30.03.20 um 23:49 schrieb Kenneth Sloan: >> This has always confused me.  After all, ImageJ does not treat PIXELS as infinitely small in x and y - so why should it consider  VOXELS to be infinitely thin in z (but with finite  width and height)? >> -- >> Kenneth Sloan >> [hidden email] >> Vision is the art of seeing what is invisible to others. >> -- >> 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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## Re: 3D projections

 Good day Kenneth, thanks for your reply! "Now...why doesn't the same logic apply to image "planes"?" With a stack of voxel-size 1x1x1 and when I use "Reslice..." (e.g. Rotate 90deg), I'm quite happy with the result. Not sure what's the original problem... Regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 31.03.20 um 18:38 schrieb Kenneth Sloan: > Understood.  Now...why doesn't the same logic apply to image "planes"? > -- > Kenneth Sloan > [hidden email] > Vision is the art of seeing what is invisible to others. > > Begin forwarded message: > >> From: Herbie <[hidden email] > >> >> Subject: Re: 3D projections >> >> Date: March 31, 2020 at 05:37:15 CDT >> >> To: [hidden email] >> >> Reply-To: [hidden email] >> >> >> "ImageJ does not treat PIXELS as infinitely small in x and y [...]" >> >> If you would, which were correct, you wouldn't see anything. >> Therefore and in general, the cheapest interpolation is applied: >> Little squares or rectangles of constant value(s). >> Actually, such block images are incorrect as well, because the correct >> interpolation is a totally different one that is much more costly and >> cannot be realized by common display technology. >> >> Regards >> >> Herbie >> >> ::::::::::::::::::::::::::::::::::::::::::: >> Am 30.03.20 um 23:49 schrieb Kenneth Sloan: >>> This has always confused me.  After all, ImageJ does not treat PIXELS >>> as infinitely small in x and y - so why should it consider  VOXELS to >>> be infinitely thin in z (but with finite  width and height)? >>> -- >>> Kenneth Sloan >>> [hidden email] >>> Vision is the art of seeing what is invisible to others. >>> -- >>> 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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## Re: 3D projections

 The problem is that confocal data is rarely cubic voxels.  They are nearly always much larger in z and x-y.  In the case of the data I was analyzing they were 0.06 x 0.06 x 0.5 µm and that is not unusual.  So you would expect to see the side on projection as a smear given you are looking through elongated voxels.  Dave Dr. David Knecht Professor, Department of Molecular and Cell Biology University of Connecticut 91 N. Eagleville Rd. U-3125 Storrs, CT 06269-3125 860-486-2200 On Mar 31, 2020, at 1:37 PM, Herbie <[hidden email]> wrote: *Message sent from a system outside of UConn.* Good day Kenneth, thanks for your reply! "Now...why doesn't the same logic apply to image "planes"?" With a stack of voxel-size 1x1x1 and when I use "Reslice..." (e.g. Rotate 90deg), I'm quite happy with the result. Not sure what's the original problem... Regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 31.03.20 um 18:38 schrieb Kenneth Sloan: Understood.  Now...why doesn't the same logic apply to image "planes"? -- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. Begin forwarded message: From: Herbie <[hidden email] > Subject: Re: 3D projections Date: March 31, 2020 at 05:37:15 CDT To: [hidden email] Reply-To: [hidden email] "ImageJ does not treat PIXELS as infinitely small in x and y [...]" If you would, which were correct, you wouldn't see anything. Therefore and in general, the cheapest interpolation is applied: Little squares or rectangles of constant value(s). Actually, such block images are incorrect as well, because the correct interpolation is a totally different one that is much more costly and cannot be realized by common display technology. Regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 30.03.20 um 23:49 schrieb Kenneth Sloan: This has always confused me.  After all, ImageJ does not treat PIXELS as infinitely small in x and y - so why should it consider  VOXELS to be infinitely thin in z (but with finite  width and height)? -- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. -- ImageJ mailing list: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Cdavid.knecht%40uconn.edu%7Cd82c64e363bb4c479b7508d7d59a6a96%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637212731502269387&sdata=nzDYjWDdPdYvAbRrrJzPhKZx3ceDKN46W3%2FBWlUdtTw%3D&reserved=0-- ImageJ mailing list: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Cdavid.knecht%40uconn.edu%7Cd82c64e363bb4c479b7508d7d59a6a96%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637212731502279382&sdata=SJU186JVMxsZqSKO9jcUk7CB%2FItPcStT7fFwKGoIShk%3D&reserved=0-- ImageJ mailing list: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Cdavid.knecht%40uconn.edu%7Cd82c64e363bb4c479b7508d7d59a6a96%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637212731502279382&sdata=SJU186JVMxsZqSKO9jcUk7CB%2FItPcStT7fFwKGoIShk%3D&reserved=0-- ImageJ mailing list: http://imagej.nih.gov/ij/list.html