Getting Imaris object is pretty similar (see previous notes).

Found several links besides Bitplane site.

Aaron Christian Pontis Qu http://www.scs2.net/home/index.php?option=com_content&view=article&id=46:qu-for-matlab&catid=34:qu&Itemid=55&showall=1

Pretty much of communication with Imaris.

• Sending 4D stack (successful with 8 z-slices, 46 timepoints tiff hyperstack)
• Retrieving spots detected in Imaris back to matlab (I waited 5 minutes but currently not responding… finally, I got all the spots, none-filtered. It took time probably because I did not filter).

How to write Matlab Code for ImarisXT: a Short Tutorial http://sybil.ece.ucsb.edu/pages/imarisxt.html

this is a bit outdated.

I will further try doing something like

• set parameters for spot detection from Matlab or Java
• do spot analysis in Imaris using above setting
• fetch the results of detected spots from Imaris to Matlab or Java
• evaluate the quality. Change spot detecton parameter
• do spot analysis again with updated parameter.
• this looping goes on until certain satisfactory value is achieved, walk through parameter space.

For this, image stack itself stays in Imaris. Only parameter setting is exported from java/matlab to imaris, and analysis results are thrown back to matlab/java.