Very basic macro for processing .lsm images

[atye]

Hello,

I've been trying to write a script that will process confocal images (.lsm), and although I've had a lot of fun trying my hand at writing a macro, I think I'm in over my head.  

To keep it simple (since I do want to learn this!), I'd like to write something that will process an opened image (e.g. "title.lsm") in the following manner:

- Split channels
- Add a scale bar to each image
- Save the images as title.tif in the same folder as the title.lsm file
- Merge the channels
- Add a scale bar to the merged image
- Save the merged image as merged-title.tif
- Close

Would a script like this add an appropriate scale bar to images that were taken under different magnifications?

Thanks for your help!

[G. Esteban Fernandez]

Yes, scale bars should be properly sized. In my experience Fiji ImageJ
opens LSM files with the proper scaling.

-Esteban
On Oct 9, 2014 3:13 PM, "atye" <[hidden email]> wrote:

> Hello,
>
> I've been trying to write a script that will process confocal images
> (.lsm),
> and although I've had a lot of fun trying my hand at writing a macro, I
> think I'm in over my head.
>
> To keep it simple (since I do want to learn this!), I'd like to write
> something that will process an opened image (e.g. "title.lsm") in the
> following manner:
>
> - Split channels
> - Add a scale bar to each image
> - Save the images as title.tif in the same folder as the title.lsm file
> - Merge the channels
> - Add a scale bar to the merged image
> - Save the merged image as merged-title.tif
> - Close
>
> Would a script like this add an appropriate scale bar to images that were
> taken under different magnifications?
>
> Thanks for your help!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Very-basic-macro-for-processing-lsm-images-tp5009985.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Yuekan Jiao-2]

Hi,

Years ago I wrote plugins to do (batch) LSM file channel splitting
and merging (but did not code the scale bar if I remember).

Just in case you are interested.

Yuekan

On Thu, Oct 9, 2014 at 5:24 PM, G. Esteban Fernandez <
[hidden email]> wrote:

> Yes, scale bars should be properly sized. In my experience Fiji ImageJ
> opens LSM files with the proper scaling.
>
> -Esteban
> On Oct 9, 2014 3:13 PM, "atye" <[hidden email]> wrote:
>
> > Hello,
> >
> > I've been trying to write a script that will process confocal images
> > (.lsm),
> > and although I've had a lot of fun trying my hand at writing a macro, I
> > think I'm in over my head.
> >
> > To keep it simple (since I do want to learn this!), I'd like to write
> > something that will process an opened image (e.g. "title.lsm") in the
> > following manner:
> >
> > - Split channels
> > - Add a scale bar to each image
> > - Save the images as title.tif in the same folder as the title.lsm file
> > - Merge the channels
> > - Add a scale bar to the merged image
> > - Save the merged image as merged-title.tif
> > - Close
> >
> > Would a script like this add an appropriate scale bar to images that were
> > taken under different magnifications?
> >
> > Thanks for your help!
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/Very-basic-macro-for-processing-lsm-images-tp5009985.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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