OpenSPIM Manual

ClearVolume & OpenSPIM usage

Prerequisites

a computer, either with Windows or OS X
a CUDA-enabled nVidia graphics card OR an OpenCL 1.1-capable graphics card with at least 1 GB of graphics memory
the latest nightly version (1.4.19) of MicroManager - see https://micro-manager.org/wiki/Micro-Manager_Nightly_Builds
an installation of Fiji (http://fiji.sc) in the same directory as MicroManager
the ClearVolume-flavoured OpenSPIM plugin, which you can download here

Installation

Installation from prepackaged plugin

After you have installed MicroManager and Fiji into the same directory, unzip the file openspim-clearvolume-SNAPSHOT.zip you have downloaded also in this file. You can verify that all the files are in the correct place if you can find a file named SPIMAcquisition.jar in [MicroManagerInstallationDirectory]/mmplugins and a file named ClearVolume-1.0.jar in [MicroManagerInstallationDirectory]/jars.

Installation from source

Using Maven

clone the source code of the plugin from the BitBucket repository.
change to the openspim-clearvolume directory and run mvn
copy the resulting SPIMAcquisition-1.0.0-SNAPSHOT.jar into your µManager plugin directory

Using IntelliJ

clone the source code of the plugin from the BitBucket repository.
open the IntelliJ project file from the openspim-clearvolume directory
in IntelliJ, edit the 'Run in MM' Run/Debug Configuration and make sure that Working directory points to your µManager installation directory (e.g./Applications/MicroManager-1.4 on OS X or C:\Program Files\MicroManager 1.4\ on Windows)
run in the 'Run in MM' configuration, µManager will open. You can run the ClearVolume-flavoured OpenSPIM plugin by clicking Acquire SPIM image in the Plugins menu.