This repository contains code for designing, analyzing, and carrying out multicolor structured illumination microscopy experiments based on a digital micromirror device (DMD-SIM), including DMD simulation code, DMD pattern generation, SIM reconstruction and instrument control. It also includes a number of useful utilities for simulating the resulting diffraction pattern given certain DMD patterns, determining system point-spread functions and optical transfer functions, and determining the affine transformation between the DMD coordinates and the imaging space coordinates. The various files are described in more detail below.
This repository is associated with the Biomedical Optics Express paper Multicolor structured illumination microscopy and quantitative control of polychromatic light with a digital micromirror device and the BioRxiv preprint. The repository state at the time of publication is archived here, or available as a release on GitHub.
When cloning this repo, use the following command to include submodules:
git clone --recurse-submodules https://github.com/QI2lab/mcSIM.git
Code for simulating the diffraction patterns produced by the DMD. Various scripts illustrating the usage of this code can be found in the examples directory
This file can be used to generate multicolor SIM patterns and other useful calibrations patterns for the DMD.
Code for reconstructing SIM images from raw data using a Gustafsson/Wiener filter style reconstruction. Several different reconstruction options are available, largely following either the approach of openSIM or fairSIM.
Code to fit the affine transformation between the DMD coordinates and camera coordinates using imaging data from a DMD pattern consisting of many small points.
Code for extracting optical transfer function from measurement of the strength of various Fourier peaks for a given SIM DMD pattern.
Code for doing the periodic/smooth image decomposition, an alternative to apodization for the Fourier transform. This code is taken from https://github.com/jacobkimmel/ps_decomp (with permission), and included here for convenience.
Miscellaneous tools for IO, reading metadata, image processing, etc.
Useful tools for automatically localizing sparse fluorescent beads and performing both 2D and 3D PSF fitting using various PSF models. Also provides useful statistics and figures summarizing the results. This code has now been split out into a separate repository which is included in this repository as a submodule for convenience.
Scripts illustrated examples of different DMD simulations and analysis are stored in examples. Associated data is located in examples/data
Code for controlling the DLP6500 DMD over USB on Windows. This code was initially based on the approaches of Lightcrafter6500DMDControl and Pycrafter6500.
This is the script used to define pattern sequences on the DMD using patterns which have been previously loaded onto the firmware using the Texas Instruments DLP6500 and DLP9000 GUI. It is a command line interface to dlp6500.py, and it is used by run_sim_triggerscop.bsh.
A beanshell script which can be run from MicroManager 2.0 Gamma to acquire SIM data using dlp6500.py to set the DMD patterns (assuming they have already been loaded into the DMD firmware as described above). This script programs a Triggerscope 3B, which then provides the analog and digital voltages required to run the rest of the experiment. The camera free runs as the master clock, triggering the Triggerscope. We use a customized version of the Triggerscope firmware V601.
This script supports collecting multidimensional data with the axis order xy-position/time/z-position/channel/SIM pattern. It also supports time-lapse imaging with arbitrary wait time.
This code was initially developed with Micro-Manager 2.0.0-gamma1 20200514, MMCore Version 10.1.0, Device API version 69, Module API version 10. But for more recent development we are using Micro-Manager 2.0.0-gamma1 20210516, MMCore Version 10.1.1, Device API version 70, Module API version 10.
MicroManager configuration file describing the equipment and settings used in the experiment.
A simple MicroManager GUI plugin for controlling the DMD patterns while "cruising around" a sample before imaging. This plugin takes input from the user and then runs set_dmd_sim.py with the appropriate arguments in a user specified Conda environment. This plugin can be compiled using IntelliJ IDEA and the resulting .jar file should be copied to the mmplugins subdirectory of the MicroManager installation directory.
Mechanical drawings of some parts used in the setup are included in the parts directory. For a more complete description of the setup and a parts list, see the published paper linked above.