For an original stack
getVoxelSize(width, height, depth, unit);
print(width, height, depth, unit);
results in
0.0493 0.0493 0.1714 microns
And there are 2 color channels and 129 Z steps.
run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=0.17
initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=50
interior=25 interpolate");
results in
1 1 1 pixels
run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=0.17
initial=330 total=60 rotation=5 lower=1 upper=255 opacity=0 surface=50
interior=25");
results in
0.0493 0.0493 0.1714 microns
Which I find interesting because shouldn't X, Y, Z all be equal, or does it not
matter because Z is an angle, not a linear distance, so we should ignore it?
Playing more with this, I think the problem is the interpolate option.
Cheers-
Michael Cammer
-----Original Message-----
From: Michael Schmid <[email protected]>
Sent: Wednesday, April 3, 2024 3:58 AM
To: [email protected]
Subject: Re: Projections losing spatial scale
[EXTERNAL]
Hi Michael,
which command do you refer to?
Image>Stacks>3D Project does keep the spatial calibration in the current
version of ImageJ. Example macro:
run("T1 Head (16-bits)");
run("3D Project...", "projection=[Brightest Point] axis=X-Axis
slice=1.50 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0
surface=100 interior=50");
(mind possible line breaks introduced by the mailer; the macro should have two
lines only)
Michael
________________________________________________________________
On 02.04.24 20:24, Cammer, Michael wrote:
> I've gotten used to projections of stacks with spatial scales assigned losing
> the spatial scales. The resulting rotations are scaled in pixels.
>
> However, I recently used an old version (years ago) of ImageJ installed on
> someone else's confocal and a resulting 3D projection did have the spatial
> scale included and correct in XY.
>
> Is the loss of the spatial scale intentional or a bug?
>
> Cheers-
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
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