Note: The code in this repository has moved into the Micro-Manager 2.0-gamma repository. Do not use it other than for the README.
Micro-Manager 2.0 plugin that opens datasets in the ClearVolume 3D viewer.
ClearVolume is a volume rendering library tailored to microscopy developed at the MPI-CBG in Dresden. The MMClearVolume plugin lets you open a ClearVolume viewer on a dataset in Micro-Manager. It only works in Micro-Manager 2.0, not in Micro-Manager 1.4
##Usage
Open a dataset in Micro-Manager. Select ClearVolume from the plugins menu. After a while, the 3D view will appear.
Change brightness and contrast using the usual Micro-Manager controls (changing the gamma by changing the histogram line
from straight to curved is especially useful). Note the ClearVolume entry in the Inspector Window. When you reduce the volume view by changing the x, y, or z slider, you can grab the active area in the slider and move it around (which will
cause the visible volume area to change).
##Usage in Live Mode When using MMClearVolume during a live, multi-D acquisition, please make sure that at least one full time point was acquired. Then set the Z position viewer in the viewer to the maximum Z value and open the ClearVolume plugin. Subsequent time points should appear in the ClearVolume viewer.
##For Developers
MMClearVolumePlugin is set-up as a Maven project. To build it, run mvn install. Copy the file MMClearVolumePlugin_-0.1-SNAPSHOT.jar in the folder
target to Micro-Manager2.0/plugins. Download all the jars needed by ClearColume by running mvn dependency:copy-dependencies which copies all dependent JARs into $target/cv_dependencies. These files can
then be copied to Micro-Manager-2.0/jars/. Look for any duplicate jars by checking the contents of plugins and mmplugins (I am not sure how important it is to remove duplicates).
##For users
Non-developers can download a recent version of the plugin (copy to the mmplugins directory) and the needed jars (extract in the Micro-Manager-2.0 directory, it will create a jars directory).
##Launching Micro-Manager Make sure that you launch Java 1.8 (ClearVolume does not work in Java 1.6, which is usually used by Micro-Manager).
###On Windows Replace the ImageJ.cfg file with something like the following:
.
..\Java\jre1.8.0_91\bin\javaw.exe
-Xmx4000m -cp .\jars\*;ij.jar ij.ImageJ
###On Linux or Mac OS X
Launch Micro-Manager by running
java -cp jars/*:ij.jar ij.ImagaJ
(in the Micro-Manager 2.0 directory).
Note the difference in the classpath separator: Linux/OSX use :, Windows uses ;.
Hopefully, installation and deployment will be much simpler in the near future!
TODOs:
- Easy deployment
- Video capture