OTSLM Toolbox for Structured Light Methods

A set of Matlab functions and graphical user interface for generating patterns for phase and amplitude spatial light modulators (SLMs) such as the digital micromirror device (DMD) and liquid crystal type device. The focus of this toolbox is on patterns for optical tweezers systems but the same functions can probably be used in other applications where amplitude or phase control of light is required.

In the initial release we include functions our group currently uses or is interested in using, but we hope that others will also contribute codes for patterns they use in research publications. If you would like to contribute patterns, we would love to hear from you, see the Contributing section bellow.

This toolbox is a work in progress. It is likely, at least in the early versions, the functions will move around, change names and behaviour. Some functions still lack documentation and might be a bit unstable. Comments and suggestions welcome.

To get started using the toolbox, take a look at the documentation. You can access the documentation online, or in the docs directory. Or, for quick installation instructions and dependendices, see bellow.

Installation and usage

To use the toolbox, download the repository and add the download directory to your path. Functions can be accessed by prefixing function names with otslm., for example

im = otslm.simple.linear([10, 10], 3);

To find out information about the functions contained in the toolbox, you can access the documentation here, in the Matlab doc browser, or access short documentation using the matlab help browser. For example

help otslm
help otslm.simple.linear

To launch the graphical user interfacces you can navigate to the corresponding file in +otslm/+ui or run the Launcher from the Matlab command line:

Dependencies

The toolbox runs on recent versions of Matlab. We have tested the toolbox and UI on Matlab 2018a.

Some functionality requires the following dependencies:

• Optical Tweezers Toolbox (1.5.1 or newer)
• Python (2.7 or newer)
  • numpy (tested on 1.13.3)
  • theano (tested on 0.9)
  • scipy (tested on 1.0)
  • pyfftw (optional, for fourier transform)
• Red Tweezers
• Specific Matlab toolboxes:
  • Optimization Toolbox
  • Signal Processing Toolbox
  • Neural Network Toolbox
  • Symbolic Math Toolbox
  • Image Processing Toolbox
  • Instrument Control Toolbox
  • Parallel Computing Toolbox
  • Image Acquisition Toolbox
• Matlab MEX compatible C++ compiler

License

If you publish work using this toolbox, please cite it as

I. C. D. Lenton, A. B. Stilgoe, T. A. Nieminen, H. Rubinsztein-Dunlop, "OTSLM toolbox for structured light methods", Computer Physics Communications, Elsevier BV, Feb. 2020, p. 107199, doi:10.1016/j.cpc.2020.107199.

This version of the code is licensed under the GNU GPLv3. Parts of the toolbox incorporate third party open source code, see the documentation, thirdparty folder and code for details about licensing of these parts.

Copyright (C) 2018 Isaac Lenton

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Further details can be found in LICENSE.md. If you would like to use the toolbox for something not covered by the license, please contact us.

Contributing

If you would like to contribute a feature, report a bug or request we add something to the toolbox, the easiest way is by creating a new issue on the OTSLM GitHub page.

If you have code you would like to submit, fork the repository, add the code and open a new issue. This method is preferable to pasting the code in the issue or sending it to us via email since your contribution details will remain attached to the commit you send (tracking authorship).

Contact us

The best person to contact for inquiries about the toolbox or licensing is Isaac Lenton

File listing

README.md     - Overview of toolbox (this file)
LICENSE.md    - License information for OTSLM original code
thirdparty/   - Third party licenses (multiple files)
examples/     - Example files showing different toolbox features
tests/        - Unit tests to verify toolbox features function correctly
docs/         - Files for building the documentation
+otslm/       - The toolbox

+otslm package, as well as tests/ and examples/ directories and sub-directories contain Contents.m files which list the files and packages in each directory. These files can be viewed in Matlab by typing help otslm or help otslm.subpackage.