Posted by
Michael Schmid on
URL: http://imagej.273.s1.nabble.com/3D-projections-tp5023114p5023123.html
Hi David,
which is the command that causes the problem?
I tried with the "Confocal Series" sample and remove the second color
channel, to get a 3D dataset (Image>Stacks>Tools>Make substack).
Then, pixel size in x&y is ~0.05 um, in z it is 0.6 um.
Image>Stacks>Orthogonal Views does it right.
Image>Stacks>Reslice interpolates unless you check 'avoid interpolation'
(then it shows it as if the voxels were cubes).
Image>Stacks>zProject does not rotate.
Among what I tried, the only one that shows thin slices is
Image>Stacks>3D project - seems this is the one you are talking about?
I had a look at it; the code (ij.plugin.projector) is not very easy to
understand. (The relevant function seems to be 'doOneProjectionY')
I fear that the author of the original Pascal version (Michael Castle,
probably > 20 years ago in the times of NIH Image, at the University of
Michigan Mental Health Research Institute) is not active in the ImageJ
community.
So I fear that the only easy solution is interpolation of the original
data (probably easiest with "reslice"), which will, of course, create a
much larger stack than what would be needed (9x the memory), then do the
"Image>Stacks>3D project".
Michael
___________________________________________________________________
On 31/03/2020 7:51 pm, Knecht, David wrote:
> 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]<mailto:
[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]<mailto:
[hidden email]> <mailto:
[hidden email]>
> Vision is the art of seeing what is invisible to others.
>
> Begin forwarded message:
>
> From: Herbie <
[hidden email]<mailto:
[hidden email]> <mailto:
[hidden email]>>
>
> Subject: Re: 3D projections
>
> Date: March 31, 2020 at 05:37:15 CDT
>
> To:
[hidden email]<mailto:
[hidden email]> <mailto:
[hidden email]>
>
> Reply-To:
[hidden email]<mailto:
[hidden email]> <mailto:
[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]<mailto:
[hidden email]> <mailto:
[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>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html