~~NOTOC~~
====== Export Hyperstack to Imaris ======

{{ :documents:ijplugin_hyperstackexporter.jpg|}}

===== Author =====

Kota Miura\\ 
Centre for Molecular and Cellular Imaging (CMCI)\\
EMBL Heidelberg\\ 
miura at embl dot de\\ 
Tel: +49 6221 387 404

===== History =====

  * 10-08-06 First Version.

===== Source =====

Released under the GNU General Public License. 

===== Requires =====

ImageJ ver 1.37j or higher ([[http://rsb.info.nih.gov/ij/upgrade/|ImageJ, upgrade page]]). 

A commercial software [[http://www.bitplane.com|Imaris (Bitplane) ver 7.0.0]] and its optional module [[http://www.bitplane.com/go/products/imarisxt|ImarisXT]]. 
===== Installation =====
 
You need to install several files. \\
  - Download **[[http://cmci.embl.de/dls/ImarisPlugin3_.jar|ImarisPlugin3_.jar]]** and place the file in the plugin folder of ImageJ. 
  - Download jacob-1.15-M3.zip from [[http://sourceforge.net/projects/jacob-project/|JACOB site]] (JACOB bridge is a module that bridges between Java and Windows application). Unzip the file and then
    * place **jacob-1.15-M3-x86.dll** (if your machine is 64-bit, then **jacob-1.15-M3-x64.dll**) in a directory where system path is set in your machine. In my case, I copied it under C:\Sun\SDK\jdk\jre\bin. 
    * place **jacob.jar** under C:\Sun\SDK\jdk\jre\lib\ext, where java path is set. 

===== Description =====

Exports multidimensional stack opened in ImageJ directly to Imaris, so that 3D time series with multiple channels could be visualized and inspected using useful interface of Imaris. It works with 8-bit and 16-bit stacks. 32-bit stack exporting should work but not tested. 

Following types of stacks could be exported:

  * Z stack
  * cz stack (up to 4 channels) 
  * RGB - Z stack  
    * each color channel will be treated as a single channel)
  * ZT stack
  * CZT stack
  * RGB - ZT stack
    * each color channel will be treated as a single channel)
     
In case of CZ, ZT, CZT, RGB-ZT stacks, stack should be already be converted to Hyperstack (Image -> Stack -> Stack to HyperStack). You should also be sure that dimensional sizes in [Image -> Image Properties] are correctly set, since plugin reads dimensional information from this. 

===== Work Flow =====

  * Open a hyperstack in ImageJ.
  * Do [Plugins -> Imaris -> Hyperstack Exporter...]. "Imaris Interface" window appears. 
  * Click "Start Imaris". Imaris application starts up. 
  * In the panel "Stack Export to Imaris", click appropriate button that matches with the dimension of your stack. Then wait for the exporting to finish. 
  * You could close this "Imaris Interface" window. Although there is check button saying "Exit Imaris when closing this dialog", Imaris survives even when ImageJ is terminated. 

===== Development =====

I noted some memos on JAVA-JACOB usage in below entries. 

http://cmci.embl.de/blogtng/2010-06-17/imaris_-_java

http://cmci.embl.de/blogtng/2010-08-03/coding_memo_for_jacob_bridge_between_java_and_bitplane_imaris

===== Acknowledgement =====

This plugin was written on top of example java application "HelloImaris.java" written by Volker Baecker, which is available in the Bitplane website.