===== Writing Matlab code for ImarisXT =====

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

Found several links besides [[http://www.bitplane.com/go/products/imarisxt/xtensions/matlab| 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this is a bit outdated.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.