Help with brightness and contrast when converting a stack to an Image5D?

[Braden]

I'm currently writing a macro that utilizes the Image5D plugin. I have a stack of ten images that represent different color channels and I use Image5D to create an RGB TIFF.

I noticed that whenever converting a stack to Image5D the display settings are automatically adjusted. Is it possible to convert a stack to Image5D without the display settings changing?

Currently I must switch from channel to channel and reset the brightness and contrast.
Thanks.

[dscho]

Hi Braden,

On Fri, 21 Jun 2013, Braden wrote:

> I'm currently writing a macro that utilizes the Image5D plugin. I have a
> stack of ten images that represent different color channels and I use
> Image5D to create an RGB TIFF.
>
> I noticed that whenever converting a stack to Image5D the display
> settings are automatically adjusted. Is it possible to convert a stack
> to Image5D without the display settings changing?

Please note that while not all features of Image5D have made it into
ImageJ 1.x itself, Image5D is no longer developed actively (Curtis Rueden
took maintainership, but that's only for critical bug fixes and
contributed enhancements).

So you will probably find it easier to use Hyperstacks instead, which
supersede the Image5D stacks.

Ciao,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Braden,

As Johannes says, Image5D is maintained, but only for critical bug fixes
and contributions from others. ImageJ's built-in hyperstacks handle most of
the common cases now.

> I have a stack of ten images that represent different color channels
> and I use Image5D to create an RGB TIFF.

Unfortunately, ImageJ 1.x's built-in hyperstacks only support up to 7
channels. So I fear Johannes's suggestion of using them for your 10-channel
data will have some wrinkles. You could write your own macro to do the
10-channel compositing, taking your 10-channel stack as input and producing
an RGB image as output. But it may be easier for you to just automate the
display range assignments using a macro (see below).

> Currently I must switch from channel to channel and reset the
> brightness and contrast.

You can avoid doing this by writing a simple macro. It should be possible
to set the displayed min/max per channel via a macro, similar to:

Stack.setPosition(1, 1, 1);
setMinAndMax(0, 100);
Stack.setPosition(2, 1, 1);
setMinAndMax(50, 150);
Stack.setPosition(3, 1, 1);
setMinAndMax(100, 200);
//...etc...

Regards,
Curtis


On Fri, Jun 21, 2013 at 4:21 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Braden,
>
> On Fri, 21 Jun 2013, Braden wrote:
>
> > I'm currently writing a macro that utilizes the Image5D plugin. I have a
> > stack of ten images that represent different color channels and I use
> > Image5D to create an RGB TIFF.
> >
> > I noticed that whenever converting a stack to Image5D the display
> > settings are automatically adjusted. Is it possible to convert a stack
> > to Image5D without the display settings changing?
>
> Please note that while not all features of Image5D have made it into
> ImageJ 1.x itself, Image5D is no longer developed actively (Curtis Rueden
> took maintainership, but that's only for critical bug fixes and
> contributed enhancements).
>
> So you will probably find it easier to use Hyperstacks instead, which
> supersede the Image5D stacks.
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html