MosaicJ on non-rectangular ROIs

[Mark Krebs]

Hi All,

I'm trying to use MosaicJ to create a mosaic of cropped images, which were created by applying a
circular mask to rectangular originals.  However, when I load the images from saved files, the images
imported into MosaicJ are rectangular, not circular.  As a consequence, proper alignment is
prevented, since the colored area outside of the circular crop dominates the alignment algorithm.  
I've tried coloring this area black or white to no avail.  Is there a way to get MosaicJ to ignore the area
outside of the crop, or is there a way to set the color of this area to "none"?

Thanks for any help.

Cheers,
Mark

[Robert Baer]

To reproduce:
1.  Open an image stack and manually do Image | Stacks | Make Montage,
setting border width to 3.
The images are separated by a white border (at least for the fluorescent
stack I used with black background).
2. Choose the "Magic Montage" toolset from the toolset selector.
3.  Make the original stack the selected image
4.  Click the "AutoMontage" tool and not the montage form (with "border
width" forced to 0)

Now try to repeat step 1 from the stack, and the border width remains at
zero and does not honor requests to return to 3.

Incidently, it would be nice to be able to set the montage panel options
(particularly border width) for the AutoMontage tool.  In any case it should
not break the capability to make a manual montage.  Still, its a
fantastically useful toolset!

Thanks,

Rob

[jmutterer]

Hi Robert,
You are right. The built-in 'Make Montage' uses a private static variable to
remember settings including border width. This means that other functions
cannot access this value for reuse. When 'automontage' is run, it uses the
default 0 border width value, and that changes the border width private
static variable from 'Make Montage'.

I am finishing a new version of the Magic Montage toolset that will handle
borders as well, and make use of the new overlay functions, so that you can
hide, show and clear whatever will be added to the figure. I'll post it
later this week.

Jerome.

On Tue, Feb 16, 2010 at 12:24 AM, Robert Baer <[hidden email]> wrote:

> To reproduce:
> 1.  Open an image stack and manually do Image | Stacks | Make Montage,
> setting border width to 3.
> The images are separated by a white border (at least for the fluorescent
> stack I used with black background).
> 2. Choose the "Magic Montage" toolset from the toolset selector.
> 3.  Make the original stack the selected image
> 4.  Click the "AutoMontage" tool and not the montage form (with "border
> width" forced to 0)
>
> Now try to repeat step 1 from the stack, and the border width remains at
> zero and does not honor requests to return to 3.
>
> Incidently, it would be nice to be able to set the montage panel options
> (particularly border width) for the AutoMontage tool.  In any case it should
> not break the capability to make a manual montage.  Still, its a
> fantastically useful toolset!
>
> Thanks,
>
> Rob
>