SLM binary mask generator for Lattice Light Sheet microscopy
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README.rst

llspy-slm: Lattice Light Sheet SLM Pattern Generator

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http://cbmf.hms.harvard.edu/wp-content/uploads/2015/07/logo-horizontal-small.png

Copyright © 2017 Talley Lambert, Harvard Medical School.


llspy-slm is a simple python app for generating binary masks to drive the spatial light modulator (SLM) on Lattice Light Sheet microscopes. It can generate both square lattices and hex lattices, and includes the ability to automatically set various parameters such as wavelength dependent beam-spacing (fully manually control is also available). Additionally, there is a batch square lattice feature that can be used to generate a large number of parameter permutations easily.

See complete usage notes in the documentation.

LLSpy SLM Pattern Generator GUI

Requirements

  • Compatible with Windows (tested on 7/10), Mac or Linux (tested on Ubuntu 16.04)
  • Python 3.6 (recommended), 3.5, or 2.7

Installation

  1. Install Anaconda

  2. Launch a terminal window (OS X, Linux), or Anaconda Prompt (Windows)

  3. Install llspy-slm:

    > conda create -n slmenv
    # for conda ≥ 4.4.0
    > conda activate slmenv
        # for conda < 4.4.0

    > activate slmenv # or on OS X / Linux > source activate slmenv

    > conda install -c talley -c conda-forge llspy-slm

    The create -n slmenv line creates a virtual environment. This is optional, but recommended as it easier to uninstall cleanly and prevents conflicts with any other python environments. If installing into a virtual environment, you must source the environment before proceeding, and each time before using llspy-slm.

  4. The gui can be launched with slmgen. You can create a bash script or batch file to autoload the environment and launch the program if desired.

    # Launch Anaconda Prompt and type...
    # for conda ≥ 4.4.0
    > conda activate slmenv
        # for conda < 4.4.0

    > activate slmenv # or on OS X / Linux > source activate slmenv

    # launch the gui > slmgen

See complete usage notes in the documentation.

Bug Reports, Feature requests, etc...

Pull requests are welcome!

To report a bug or request a feature, please submit an issue on github