FIJI 2D stitching in a macro

Posted by Jacqueline Ross on Nov 15, 2010; 8:52pm
URL: http://imagej.273.s1.nabble.com/Advice-petition-on-learning-java-programming-tp3686421p3686425.html

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/