Re: FIJI 2D stitching in a macro

Posted by Stephan Preibisch on Nov 16, 2010; 1:02am
URL: http://imagej.273.s1.nabble.com/Advice-petition-on-learning-java-programming-tp3686421p3686426.html

Hi,

you should be able to record a macro that stores what allowed you to merge
it for one timepoint. In the ideal case you simple make a loop over the 1000
images and it should be fine. At which point are you stuck?

Nice greetings,
Stephan

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jacqui Ross
> Sent: Montag, 15. November 2010 21:53
> To: [hidden email]
> Subject: FIJI 2D stitching in a macro
>
> Dear All,
>
> One of our users has acquired time-lapse data on a Nikon BioStation
> that
> she now wants to merge into a movie. She has acquired 3 images at each
> time point, which can be merged together nicely using the 2D Stitch
> plugin.
>
> However, there are over 1000 sets of images ("top", "middle" and
> "bottom") to be merged.
>
> Is anyone able to let me know how I can put this into a macro? We have
> 3
> data sets of tiff files sequentially named in 3 individual folders,
> top,
> middle and bottom. The tiling is not straightforward in that it is like
> a zigzag rather than a rectangle. However, the 2D plugin did merge the
> 3
> images very well so if we can automate the procedure and obtain the
> merged tiff files for each time point, we can then easily build the
> AVI.
>
> I have looked at the batch processing options but I haven't figured out
> how to select the correct images.
>
> Thanks in advance for any assistance.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/