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README.md

multicolorSIM

Code for running a multicolor SIM experiment using a DLP6500 DMD and performing SIM reconstruction. This package 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 relevant files are described in more detail below.

Preprint: Multicolor structured illumination microscopy and quantitative control of coherent light with a digital micromirror device

Hardware control code

set_dmd_sim.py

This is the script used to set certain pattern sequences on the DMD from patterns which have been previously loaded onto the firmware using the Texas Instruments DLP6500 and DLP9000 GUI

mcsim/instruments/dlp6500.py

Code for controlling the DLP6500 DMD over USB. This code was initially based on https://github.com/mazurenko/Lightcrafter6500DMDControl, and several functions are based on https://github.com/csi-dcsc/Pycrafter6500

run_sim_triggerscope.bsh

This is a bean shell script which can be run from MicroManager2.0 Gamma to acquire SIM data. It programs the DMD by calling to the python code in this repository, and programs the Triggerscope, which synchronizes the instruments.

SIM.cfg

Configuration file describing experimental equipment to MicroManager

analysis and simulation code

mcsim/affine.py

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.

mcsim/dmd_patterns.py

This file can be used to generate multicolor SIM patterns and other useful calibrations patterns for the DMD.

mcsim/fit_psf.py

Code for automatically finding PSF spots on an image of a sparse bead slide, performing both 2D and 3D PSF fitting using various PSF models, and providing useful statistics and figures summarizing the results.

mcsim/otf_tools.py

Code for extracting optical transfer function from measurement of the strength of various Fourier peaks for a given SIM DMD pattern.

mcsim/sim_reconstruction.py

Code for reconstructing SIM images from raw data

mcsim/simulate_dmd.py

Code for simulating the diffraction patterns produced by the DMD

mcsim/psd/psd.py

Code for doing the periodi/smooth image decomposition, an alternative to apodization for the Fourier transform. This code is taken from https://github.com/jacobkimmel/ps_decomp, and include here for convenience.

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Code for running a multicolor SIM experiment using a DLP6500 DMD and performing SIM reconstruction.

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