A question about virtual 5D opener plug in

[michele caccia]

Dear all
I've a problem with Virtual 5D Opener on my new Mac. I think the plug does
not "speak" correctly with the new operating system by Apple: Lion. I tried
3 different version of ImageJ: 1.43o, 1.45r and 1.46c but no one opens
correctly 5D data. Moreover all these versions don't work well with the
sample file present in the Open menu of ImageJ too; in fact if you try to
open the sample 5D file, called "mitosis", you expect something like that
reported at page 12 of, for example, the ImageJ user guide of version 1.45m
(see also attachment1.png); instead you get something like that in the png
attachment2 file. Note that the arrows at the side of the Channel and Z
scroll-bar are not present. this is very annoying because it does not allow
you to move across your file frame by frame. Does someone have the same
problem? Is there a solution or another plugin useful for 5D files?
Note that on the old version of apple operating systems imageJ1.43o works
well.
Thank you in advance for your suggestions.

Mic.

[John Oreopoulos]

Hi Michele,

This may be the same Lion OS scrollbar issue that was discussed a little while ago when the new OS came out:

http://imagej.588099.n2.nabble.com/Mac-OS-Lion-and-ImageJ-td6601294.html

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca


On 2011-12-22, at 9:29 AM, michele caccia wrote:

> Dear all
> I've a problem with Virtual 5D Opener on my new Mac. I think the plug does
> not "speak" correctly with the new operating system by Apple: Lion. I tried
> 3 different version of ImageJ: 1.43o, 1.45r and 1.46c but no one opens
> correctly 5D data. Moreover all these versions don't work well with the
> sample file present in the Open menu of ImageJ too; in fact if you try to
> open the sample 5D file, called "mitosis", you expect something like that
> reported at page 12 of, for example, the ImageJ user guide of version 1.45m
> (see also attachment1.png); instead you get something like that in the png
> attachment2 file. Note that the arrows at the side of the Channel and Z
> scroll-bar are not present. this is very annoying because it does not allow
> you to move across your file frame by frame. Does someone have the same
> problem? Is there a solution or another plugin useful for 5D files?
> Note that on the old version of apple operating systems imageJ1.43o works
> well.
> Thank you in advance for your suggestions.
>
> Mic.
> <Attachment1.png><Attachment2.png>

[Rasband, Wayne (NIH/NIMH) [E]]

On Dec 22, 2011, at 9:29 AM, michele caccia wrote:

> Dear all
> I've a problem with Virtual 5D Opener on my new Mac. I think the plug does
> not "speak" correctly with the new operating system by Apple: Lion. I tried
> 3 different version of ImageJ: 1.43o, 1.45r and 1.46c but no one opens
> correctly 5D data. Moreover all these versions don't work well with the
> sample file present in the Open menu of ImageJ too; in fact if you try to
> open the sample 5D file, called "mitosis", you expect something like that
> reported at page 12 of, for example, the ImageJ user guide of version 1.45m
> (see also attachment1.png); instead you get something like that in the png
> attachment2 file. Note that the arrows at the side of the Channel and Z
> scroll-bar are not present. this is very annoying because it does not allow
> you to move across your file frame by frame. Does someone have the same
> problem? Is there a solution or another plugin useful for 5D files?
> Note that on the old version of apple operating systems imageJ1.43o works
> well.
> Thank you in advance for your suggestions.

You can use the "<" and ">" keyboard shortcuts, or the left or right arrow keys if there is no selection, as a substitute for the arrows Apple removed in Lion. Hold down the control key to move through slices and the alt key down to move through frames.

-wayne

[michele caccia]

Dear all
This solution is good just for what concerns the example file mitosis. But
I'm enjoying with time lapse data from a 7 days experiment. in every series
you have 3 channels, 5 Z stacks, 168 time points and 99 positions. As you
can see they are "6 dimensions data"; anyway if you use virtual image 5D
opener following the instructions by Mario (see
http://imagej.588099.n2.nabble.com/Import-array-of-images-as-ImageSequence-td3857750.html)
it is quiet simple to manage the data.
You have a "T-scroll-bar" that manages Z stacks and Position Number, the "Z
scroll-bar" that manages time and  the channel at the right side of your
image (see attachment).
With the old versions of Mac OS you had the arrows at the side of the
scroll-bars, in Lion you can hold whatever you want: ctrl, alt or command
key but you always manage the upper scroll-bar named as Z.
Does someone have the same problem? is there an alternative plug-in?
thank you again.

MIc


2011/12/23 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>

> On Dec 22, 2011, at 9:29 AM, michele caccia wrote:
>
> > Dear all
> > I've a problem with Virtual 5D Opener on my new Mac. I think the plug
> does
> > not "speak" correctly with the new operating system by Apple: Lion. I
> tried
> > 3 different version of ImageJ: 1.43o, 1.45r and 1.46c but no one opens
> > correctly 5D data. Moreover all these versions don't work well with the
> > sample file present in the Open menu of ImageJ too; in fact if you try to
> > open the sample 5D file, called "mitosis", you expect something like that
> > reported at page 12 of, for example, the ImageJ user guide of version
> 1.45m
> > (see also attachment1.png); instead you get something like that in the
> png
> > attachment2 file. Note that the arrows at the side of the Channel and Z
> > scroll-bar are not present. this is very annoying because it does not
> allow
> > you to move across your file frame by frame. Does someone have the same
> > problem? Is there a solution or another plugin useful for 5D files?
> > Note that on the old version of apple operating systems imageJ1.43o works
> > well.
> > Thank you in advance for your suggestions.
>
> You can use the "<" and ">" keyboard shortcuts, or the left or right arrow
> keys if there is no selection, as a substitute for the arrows Apple removed
> in Lion. Hold down the control key to move through slices and the alt key
> down to move through frames.
>
> -wayne
>