FARSIGHT Tutorials/Building Software/Bio-Formats/UsrTutorial

This tutorial is designed for end users who have no need to modify the source code of Bio-Formats or FARSIGHT. Using these instructions, you will simply download pre-built versions of FARSIGHT and Bio-Formats so that they can be used immediately for image analysis. If you would prefer instructions for downloading the source code and compiling these components manually, you can pick an appropriate developer tutorial from the tutorials page.

If you have any problems during this process, please contact the bio-formats team.

Step 1: Download and Install FARSIGHT

• Go to the FARSIGHT downloads page.
• Select your operating system.
• Select the file to download (likely the most recent stable release).
• Depending on your chosen OS, you will either:
  • Run the downloaded installer and follow its step-by-step instructions.
  • Extract the downloaded archive to a path of your choice.

FARSIGHT is now installed!

Step 2: Download Bio-Formats

• Go to the Bio-Formats downloads page.
• In the "Bio-Formats ITK Plugin Libraries (for end users)" section, download the zipped binaries folder appropriate for your operating system.
• Extract the contents of the zipped archive to a location of your choice (e.g. if you were using Windows, you might extract the contents to C:\Bioformats). From this point, the instructions will depend on your operating system:
• Mac, 32-bit Linux: There is no corresponding FARSIGHT release for these operating systems, so the BF-ITK downloads only contain the BF-ITK libraries. You will need to set two environment variables for the plug-in to work.
  • Set the environment variable ITK_AUTOLOAD_PATH to the location where you extracted the binaries in the previous step. This is done with the terminal command:
  • export ITK_AUTOLOAD_PATH="<replace_with_path_to_binaries>"
  • Set the environment variable LD_LIBRARY_PATH (on Linux) or DYLD_LIBRARY_PATH (on Mac) to the same path as above.
• 64-bit Linux: you will see an "exe" and "lib" subdirectories in your BF-ITK download.
  • Copy all the files in the "exe" subdirectory to <path-to-Farsight-download>/Farsight-0.3.3-Linux/bin
  • In your terminal, navigate to the "lib" subdirectory and execute the command: sudo cp * /usr/lib to copy all the files to your lib directory.
  • Set the environment variables ITK_AUTOLOAD_PATH and LD_LIBRARY_PATH to <path-to-Farsight-download>/Farsight-0.3.3-Linux/bin via the terminal command: export <VARIABLE_NAME>="<NEW_VALUE>"
  • BF-ITK is now installed!
• Windows: see this page.

The ITK Bio-Formats plugin is now set up!

Using Bio-Formats with FARSIGHT

You don't need to do anything special to use the Bio-Formats plug-in with any FARSIGHT module. Simply setting the ITK_AUTOLOAD_PATH environment variables allows the ITK-based FARSIGHT modules (and, in fact, any other ITK-based applications you may use) to automatically take advantage of Bio-Formats' capacity for opening an extensive variety of image types.

If you ever wish to disable Bio-Formats, you can do by simply setting the ITK_AUTOLOAD_PATH to "".

An *.ids format image, unsupported by ITK, opened in the FARSIGHT Nucleus Editor with Bio-Formats.