[ImageJ-devel] loading imageJ instance with full Services

[Curtis Rueden]

Hi Mohamed and everyone,

I agree with Johannes that using "new ImageJ()" is better for programmatic
use, in that it is more flexible. That said, there is nothing "wrong" per
se with calling "imagej.Main.launch()" if what you really want is for the
ImageJ application to pop up. So no worries there.

As for your reported problem, I have a couple of questions:

> If I use this instance to open an lsm image with 2 channels

Please note that ImageJ2 does not support LSM out of the box. You need
either Bio-Formats or LSM_Reader for that (which at the moment are ImageJ1
plugins, and will be run using the IJ2's legacy layer). If you open an LSM
with File > Open right now, I believe it will open as a vanilla TIFF file,
which may not read all the metadata, and may misinterpret some
Zeiss-specific image parameters.

> Note that opening the imageJ from the provided executable works fine.

Hmm, you mean if you launch ImageJ2 from the launcher, then open your LSM
file, it behaves as expected? Then there may indeed be a bug lurking here
somewhere. Do you have a sample non-working image file you can upload via
the Help > Upload Sample Image command? That, along with specific brief
instructions about what doesn't work, would be very helpful to diagnose and
fix the problem.

Thanks,
Curtis


On Mon, Jun 24, 2013 at 9:54 AM, Mohamed Tleis <mohammedtleis at hotmail.com>wrote:

> Dear Developers,
>
> from inside my code I am calling imageJ through
>
> ImageJ ij = new ImageJ.Main.launch();
>
> If I use this instance to open an lsm image with 2 channels, the image
> isn't loaded properly, only one channel is visable and trying to split
> channels will ask me for arguments and won't be done.
> Note that opening the imageJ from the provided executable works fine. I
> suppose the launch method needs some arguments to be passed. Can you please
> show me an example to how to do this?
>
> Best Regards,
> M. Tleis
>
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