arbitrary rotation of an image z stack around one axis only

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arbitrary rotation of an image z stack around one axis only

Guenter Giese
Dear list members,

 

I would like to display individual planes after arbitrary rotation of an
image z stack around either the y or the x axis (one axis only each time,
maybe two in sequence).

 

I tried the Plugins > Transform > Interactive Stack Rotation. This does the
job, but using the mouse I would have to move straight to the left / right
or to top / bottom (one axis only) to change one angle only, which is almost
impossible to do interactively. I always change both angles.

 

I tried to engage the X, Y or Z key as suggested on the Fiji web site, but
this does not help.

 

How to change interactively only one angle /one after each other?

 

Is there any display of the angles moved from start into each direction? Can
this be recorded, e.g. by the macro recorder?

 

Best,

 

Guenter

 

 

Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung
D-69120 Heidelberg, Germany
phone  xx49 or 0 -6221-486-360  fax -325
e-mail:  <mailto:[hidden email]>
[hidden email]

 


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Re: arbitrary rotation of an image z stack around one axis only

Stephan Saalfeld
Hi Guenter,

> I tried the Plugins > Transform > Interactive Stack Rotation. This does the
> job, but using the mouse I would have to move straight to the left / right
> or to top / bottom (one axis only) to change one angle only, which is almost
> impossible to do interactively. I always change both angles.
>
> I tried to engage the X, Y or Z key as suggested on the Fiji web site, but
> this does not help.
>

Not for using the mouse.  With X, Y, Z, you select the axis of rotation
for subsequent rotation with the left and right cursor keys.  Put the
mouse aside and use the cursor keys.  

> How to change interactively only one angle /one after each other?
>

With the left and right cursor keys and X, Y, Z.  The angle is 1deg
without modifier keys, 0.1deg with Ctrl and 10deg with Shift.

>
>
> Is there any display of the angles moved from start into each direction? Can
> this be recorded, e.g. by the macro recorder?
>

No, but knowing the numbers above you can count your keystrokes.
Pressing Cursor left + Shift 9 times is a 90deg rotation around the
previously selected axis.

With the E key, you can print the affine rotation matrix into the IJ log
for subsequent use in other transformation tools.

Best,
Stephan

>
>
> Best,
>
>  
>
> Guenter
>
>  
>
>
>
> Dr. Guenter Giese
> Light Microscopy Facility Manager
> Dept. of Biomedical Optics
> MPI fuer Medizinische Forschung
> D-69120 Heidelberg, Germany
> phone  xx49 or 0 -6221-486-360  fax -325
> e-mail:  <mailto:[hidden email]>
> [hidden email]
>
>  
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: arbitrary rotation of an image z stack around one axis only

Guenter Giese
Thank you, Stephan,

this works.


Guenter

Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung
D-69120 Heidelberg, Germany
phone  xx49 or 0 -6221-486-360  fax -325
e-mail: [hidden email]

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Stephan Saalfeld
> Sent: Mittwoch, 11. Dezember 2013 17:36
> To: [hidden email]
> Subject: Re: arbitrary rotation of an image z stack around one axis only
>
> Hi Guenter,
>
> > I tried the Plugins > Transform > Interactive Stack Rotation. This
> > does the job, but using the mouse I would have to move straight to the
> > left / right or to top / bottom (one axis only) to change one angle
> > only, which is almost impossible to do interactively. I always change both
> angles.
> >
> > I tried to engage the X, Y or Z key as suggested on the Fiji web site,
> > but this does not help.
> >
>
> Not for using the mouse.  With X, Y, Z, you select the axis of rotation for
> subsequent rotation with the left and right cursor keys.  Put the mouse aside
> and use the cursor keys.
>
> > How to change interactively only one angle /one after each other?
> >
>
> With the left and right cursor keys and X, Y, Z.  The angle is 1deg without
> modifier keys, 0.1deg with Ctrl and 10deg with Shift.
>
> >
> >
> > Is there any display of the angles moved from start into each
> > direction? Can this be recorded, e.g. by the macro recorder?
> >
>
> No, but knowing the numbers above you can count your keystrokes.
> Pressing Cursor left + Shift 9 times is a 90deg rotation around the previously
> selected axis.
>
> With the E key, you can print the affine rotation matrix into the IJ log for
> subsequent use in other transformation tools.
>
> Best,
> Stephan
> >
> >
> > Best,
> >
> >
> >
> > Guenter
> >
> >
> >
> >
> >
> > Dr. Guenter Giese
> > Light Microscopy Facility Manager
> > Dept. of Biomedical Optics
> > MPI fuer Medizinische Forschung
> > D-69120 Heidelberg, Germany
> > phone  xx49 or 0 -6221-486-360  fax -325
> > e-mail:  <mailto:[hidden email]>
> > [hidden email]
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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