Automation Stack Processing

[Aedifex]

Hi Im currently working on a long term observation setup for stem cells which generates big image sequences in an interval defined by the user. Usually I end up with somewhat around 1200 pictures, my problem is that im measuring both bright field and fluorescence and that i need to overlay the fluorescence images with the corresponding bright field measurement at 50% opacity (the first image is always bright, the second fluorescence). I was wondering if it would be possible to automate this work with a macro in imagej but im biologist and not very good at programming. It would be great if someone could help me out with that.

[gankaku]

Hi Rouven,

The best way to get the overlay (or superimposed image) as you might need
it is via the function >Image >Color >Merge channels...
If you have the complete stacks of your two channels you can just assign
them in the merge channels dialog to the respective color channels you want
them to be displayed (most likely gray and another color). This works for
complete stacks in one go.

You can also macro record these commands for later reuse under >Plugins
>Macros >Record...

But since it records the absolute file names that need some manual
adjustment in the macro. So for the beginning you can first start the
manual merging and use the macro recorder to get insight into the macro
language.

Further information on macro command you can find here:
http://rsbweb.nih.gov/ij/developer/macro/functions.html

regards,
Jan

2016-05-09 13:39 GMT+02:00 Aedifex <[hidden email]>:

> Hi Im currently working on a long term observation setup for stem cells
> which
> generates big image sequences in an interval defined by the user. Usually I
> end up with somewhat around 1200 pictures, my problem is that im measuring
> both bright field and fluorescence and that i need to overlay the
> fluorescence images with the corresponding bright field measurement at 50%
> opacity (the first image is always bright, the second fluorescence). I was
> wondering if it would be possible to automate this work with a macro in
> imagej but im biologist and not very good at programming. It would be great
> if someone could help me out with that.
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Automation-Stack-Processing-tp5016362.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

CEO: Dr. rer. nat. Jan Brocher
phone:  [phone]
mobile: [phone]
e-mail: [hidden email]
info: [hidden email]
inquiries: [hidden email]
web: www.biovoxxel.de

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

[Aedifex]

Hi Jan,

thanks for your advice ill give it a try!