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Timothy Blattner edited this page Nov 13, 2023 · 10 revisions

MIST Plugin Installation

Installing the plugin into Fiji is simplified using Fiji's update site manager. If the machine is not configured for the network then please refer to the manual installation.

Update Site Installation

  1. Open Fiji
  2. Help >> Update Fiji (or "Update...")
  3. Manage update sites
  4. Activate MIST by selecting check box
  5. Close and Apply Changes
  6. Restart Fiji
  7. Plugin is installed in Plugin >> Stitching >> MIST

Or

  1. Open Fiji
  2. Help >> Update Fiji (or "Update...")
  3. Manage update sites
  4. Click "Add"
  5. Enter Name: "MIST" and URL: http://sites.imagej.net/NIST-ISG-MIST/
  6. Close and Apply Changes
  7. Restart Fiji
  8. Plugin is installed in Plugin >> Stitching >> MIST

Manual Installation

  1. Download the latest version of the MIST plugin from MIST Plugin Download
  2. Extract the contents of the zip file into your Fiji.app folder
  3. Restart Fiji
  4. Plugin is installed in Plugins >> Stitching >> MIST

FFTW Installation

FFTW (Fastest Fourer Transform in the West, http://fftw.org ) is a C implementation out of MIT that computes the discrete Fourier transform. The plugin loads the library at run-time and uses the high performance FFTW functions in Java.

Requirements:

  1. Fiji (64-bit version)

Note: 64-bit Windows systems should be able to run the FFTW version without additional setup.

FFTW Installation on Unix (64-bit Mac OSX/Linux)

  1. Download fftw-3.3.4.tar.gz from http://www.fftw.org/download.html
  2. Extract source code to directory (terminal command: "tar -xzvf fftw-3.3.4.tar.gz")
  3. From a terminal locate source code and run the following commands to compile the 32bit and 64bit versions:
    ./configure --enable-shared
    make
    sudo make install
    ./configure --enable-float --enable-shared
    make
    sudo make install

(If configure fails, additional compilers and/or libraries may be needed)

  1. Launch the Fiji MIST plugin
  2. Specify the FFTW library file in the Advanced FFTW Options FFTW options user guide (default FFTW installation location is in /usr/local/lib)
  3. Linux library name example: libfftw3.so (or similar)
  4. MacOSX library name example: libfftw3.dylib (or similar)
  5. You should now be able to launch MIST using FFTW

FFTW Installation using MacPorts

  1. From the command-line: sudo port install fftw-3
  2. Launch the Fiji MIST plugin
  3. Specify the FFTW library file in the Advanced FFTW Options FFTW options user guide (default FFTW installation location is in /usr/local/lib)
  4. Linux library name example: libfftw3.so (or similar)
  5. MacOSX library name example: libfftw3.dylib (or similar)
  6. You should now be able to launch MIST using FFTW

CUDA Installation

Due to GPU architectural changes, we no longer support the CUDA version of MIST.

CUDA is the Compute Unified Device Architecture and is a language developed by NVIDIA. It is used to execute code on NVIDIA GPUs to obtain high performance.

Requirements:

  1. NVIDIA GPU installed on your system (compute capability 3.0 or better, equivalent to Kepler architecture or newer, currently Volta-class GPUs have undefined behavior)
  2. CUDA toolkit version 9.0
  3. Fiji 64-bit

Once the CUDA toolkit is installed a computer restart might be required before stitching can take advantage of your GPU.

CUDA Toolkit v9.0 installation on Windows/Linux/MacOSX

  1. Download CUDA toolkit v9.0 for the appropriate operating system version CUDA Toolkit 9.0
  2. Install the CUDA Tookit
  3. For Windows: Launch the executable and complete the installation
  4. For MacOSX: Toolkit MacOSX installation guide
  5. For Linux: Toolkit Linux installation guide
  6. Restart your computer
  7. Open Fiji and run MIST plugin
  8. CUDA option should be available in the MIST plugin.

How to modify MIST to use an older or newer version of CUDA

  1. (Optional/Recommended) Download Intellij
  2. Clone 'https://github.com/usnistgov/MIST.git' onto your machine (Can be done within Intellij)
  3. Open pom.xml and edit the dependency entries for jcuda and jcufft to desired version number (Available versions)
  4. Reload/Update Imports for Maven
  5. Extract jcuda and jcufft native libraries from "<path/to/home>/.m2/repositories/org/jcuda" for both "jcuda-natives" and "jcufft-natives"
  6. Add extracted libraries into "<MIST_HOME>/lib/jcuda" (dll for Windows and .so for Linux)
  7. Generate project files (In IntelliJ "Build/Build Artifacts/All Artifacts")
  8. Copy contents of "<MIST_HOME>/out/artifacts/MIST_Fiji" into Fiji.app
  9. Copy native libraries from "<MIST_HOME>/lib/jcuda" into "Fiji.app/lib/jcuda"
  10. Launch Fiji and it should now use the new versions of JCuda

Compilation from source

  1. (Optional/Recommended) Download Intellij
  2. Clone 'https://github.com/usnistgov/MIST.git' onto your machine (Can be done within Intellij)
  3. Reload/Update Maven
  4. Run maven package (mvn package) for MIST. This will generate three jar files in a newly created target directory.
  5. Navigate to MIST/target directory. Execute using "java -jar MIST_-.-jar-with-dependencies.jar"

If you receive a warning about 32-bit execution, please install a 64-bit version of java, and run using that version.

For instructions on how to execute MIST from command-line: https://github.com/usnistgov/MIST/wiki/User-Guide#command-line-execution-of-mist

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