Converting a stack to a montage

[Dutton,Jeff]

I am attempting to convert a group of 5 image stacks into a 2-column, 3-row
montages.  I have the border set to 3 as well.  I am encountering a bit of
inconsistency in how the montage is made with regard to the empty spot in
the lower right corner.  At times, the montage has a white lower right
corner and the borders are black.  This is the way I would like it.  At
other times the lower right corner is black and the borders are white.  Is
there a way to force some kind of consistent behavior?  I have a plugin
that I have written to assemble about 150 of these montages but if they are
not consistent it will still create a lot of hand work.

What determines the border and blank space behavior as far as color choices
made by the program?

Any info would be apprecaited.

Jeff

[Wayne Rasband]

> I am attempting to convert a group of 5 image stacks into a
> 2-column, 3-row montages.  I have the border set to 3 as
> well.  I am encountering a bit of inconsistency in how the
> montage is made with regard to the empty spot in the lower
> right corner.  At times, the montage has a white lower right
> corner and the borders are black.  This is the way I would
> like it.  At other times the lower right corner is black and
> the borders are white.  Is there a way to force some kind of
> consistent behavior?  I have a plugin that I have written to
> assemble about 150 of these montages but if they are not
> consistent it will still create a lot of hand work.
>
> What determines the border and blank space behavior as far
> as color choices made by the program?

With 16 and 32 bit images, Image>Stacks>Make Montage always draws white
borders and labels and fills unused areas with black. With 8 bit and
RGB images, it draws in white and fills with black if the median pixel
value of the first slice is less than 200, otherwise it draws in black
and fills with white. With ImageJ 1.35m and later, there is an option
to draw in the foreground color and fill with the background color.

-wayne

[No Name-4]

Wayne,

Is ImageJ 1.35m available? The most recent version that I see is 1.35l. I
would love to have the ability to select the border and text color. Right
now, my workaround is to make a duplicate image of the montage, threshold
to create a black 'border only' image and do Image Calculator to AND the
images.

Thanks,
Jim Deeds





Wayne Rasband <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
01/18/2006 03:48 PM
Please respond to ImageJ Interest Group

 
        To:     [hidden email]
        cc:     (bcc: James Deeds/PH/Novartis)
        Subject:        Re: Converting a stack to a montage

> I am attempting to convert a group of 5 image stacks into a
> 2-column, 3-row montages.  I have the border set to 3 as
> well.  I am encountering a bit of inconsistency in how the
> montage is made with regard to the empty spot in the lower
> right corner.  At times, the montage has a white lower right
> corner and the borders are black.  This is the way I would
> like it.  At other times the lower right corner is black and
> the borders are white.  Is there a way to force some kind of
> consistent behavior?  I have a plugin that I have written to
> assemble about 150 of these montages but if they are not
> consistent it will still create a lot of hand work.
>
> What determines the border and blank space behavior as far
> as color choices made by the program?

With 16 and 32 bit images, Image>Stacks>Make Montage always draws white
borders and labels and fills unused areas with black. With 8 bit and
RGB images, it draws in white and fills with black if the median pixel
value of the first slice is less than 200, otherwise it draws in black
and fills with white. With ImageJ 1.35m and later, there is an option
to draw in the foreground color and fill with the background color.

-wayne

[Wayne Rasband]

> Is ImageJ 1.35m available? The most recent version that I
> see is 1.35l. I would love to have the ability to select the
> border and text color. Right now, my workaround is to make a
> duplicate image of the montage, threshold to create a black
> 'border only' image and do Image Calculator to AND the
> images.

ImageJ 1.35m is now available at
"http://rsb.info.nih.gov/ij/notes.html".

-wayne

[Dutton,Jeff]

Thank you very much for the information and the software update.  It
functions beautifully!

Jeff

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wayne Rasband
Sent: Wednesday, January 18, 2006 3:48 PM
To: [hidden email]
Subject: Re: Converting a stack to a montage

> I am attempting to convert a group of 5 image stacks into a
> 2-column, 3-row montages.  I have the border set to 3 as
> well.  I am encountering a bit of inconsistency in how the
> montage is made with regard to the empty spot in the lower
> right corner.  At times, the montage has a white lower right
> corner and the borders are black.  This is the way I would
> like it.  At other times the lower right corner is black and
> the borders are white.  Is there a way to force some kind of
> consistent behavior?  I have a plugin that I have written to
> assemble about 150 of these montages but if they are not
> consistent it will still create a lot of hand work.
>
> What determines the border and blank space behavior as far
> as color choices made by the program?

With 16 and 32 bit images, Image>Stacks>Make Montage always draws white
borders and labels and fills unused areas with black. With 8 bit and
RGB images, it draws in white and fills with black if the median pixel
value of the first slice is less than 200, otherwise it draws in black
and fills with white. With ImageJ 1.35m and later, there is an option
to draw in the foreground color and fill with the background color.

-wayne