GNU Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Being an array programming language, it is naturally suited for image processing and handling of N dimensional datasets. Octave is distributed under the terms of the GNU General Public License.

The Octave language is Matlab compatible so that programs are easily portable. Indeed, the Octave bioformats package is exactly the same as Matlab’s, the only difference being the installation steps.

Requirements

The bioformats package requires Octave version 4.0.0 or later with support for java:

$ octave
>> OCTAVE_VERSION
ans = 4.0.0
>> usejava ("jvm")
ans =  1

Installation

  1. Download bioformats_package.jar and place it somewhere sensible for your system (in Linux, this will probably be /usr/local/share/java or ~/.local/share/java for a system-wide or user installation respectively).

  2. Add bioformats_package.jar to Octave’s static javaclasspath (see Octave’s documentation).

  3. Download the Octave package.

  4. Start octave and install the package with:

    >> pkg install path-to-bioformats-octave-version.tar.gz

Usage

Usage instructions are the same as Matlab. The only difference is that you need to explicitly load the package. This is done by running at the Octave prompt:

>> pkg load bioformats

Upgrading

To use a newer version of Bio-Formats, repeat the install instructions. Do not follow the Matlab instructions.