├── .gitattributes ├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── calibration ├── fit_hologram_phase_curvature.py ├── odt_align_frqs.py ├── psf_calibration.py └── sim_modulation_depth_from_beads.py ├── docs ├── Makefile ├── conf.py ├── daq.rst ├── dlp6500.rst ├── dmd_affine.rst ├── dmd_patterns.rst ├── dmd_simulation.rst ├── fft.rst ├── field_prop.rst ├── gauss_beam.rst ├── index.rst ├── make.bat ├── mie_fields.rst ├── optimize.rst ├── otf_tools.rst ├── phase_unwrap.rst ├── sim.rst └── tomography.rst ├── examples ├── calibrate_affine_xform.py ├── dmd_solution_explorer_gui.py ├── find_multicolor_sim_patterns.py ├── load_dmd_pattern.py ├── reconstruct_sim_experiment_multichannel.py ├── reconstruct_sim_gpu_repeatedly.py ├── reconstruct_sim_simulated_single.py ├── reconstruct_sim_simulated_timelapse.py ├── simulate_dmd_diffraction_fourier_plane.py ├── simulate_dmd_diffraction_pattern.py ├── simulate_multicolor_sim_patterns_1d.py └── solve_multicolor_blaze_condition.py ├── mcsim ├── __init__.py ├── analysis │ ├── __init__.py │ ├── camera_noise.py │ ├── dmd_patterns.py │ ├── fft.py │ ├── field_prop.py │ ├── fit_dmd_affine.py │ ├── gauss_beam.py │ ├── mie_fields.py │ ├── odt_patterns.py │ ├── optimize.py │ ├── otf_tools.py │ ├── phase_unwrap.py │ ├── sim_reconstruction.py │ ├── simulate_dmd.py │ ├── tomography.py │ └── visualize.py └── expt_ctrl │ ├── __init__.py │ ├── blackfly_flir_cam.cfg │ ├── config.json │ ├── daq.py │ ├── dlp6500.py │ ├── phantom_cam.py │ ├── program_sim_odt.py │ ├── setup_optotune_mre2.py │ ├── sim_odt_nidaq_c1.cfg │ └── sim_odt_nidaq_c2.cfg ├── parts_list.md ├── pyproject.toml └── tests ├── dmd_pattern_unittest.py ├── mie_unittest.py ├── sim_unittest.py └── tomography_unittest.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/mcSIM/HEAD/.gitattributes -------------------------------------------------------------------------------- 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