Beads simulator for AOViFT

Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens

Thayer Alshaabi^1,2*, Daniel E. Milkie¹, Gaoxiang Liu², Cyna Shirazinejad², Jason L. Hong², Kemal Achour², Frederik Görlitz², Ana Milunovic-Jevtic², Cat Simmons², Ibrahim S. Abuzahriyeh², Erin Hong², Samara Erin Williams², Nathanael Harrison², Evan Huang², Eun Seok Bae², Alison N. Killilea², David G. Drubin², Ian A. Swinburne², Srigokul Upadhyayula^2,3,4*, Eric Betzig^1,2,5*

¹HHMI, ²UC Berkeley, ³Lawrence Berkeley National Laboratory, ⁴Chan Zuckerberg Biohub, ⁵Helen Wills Neuroscience Institute

Installation
Features

Installation

Dependencies

Important

Source code is tested on the following operating systems:

Ubuntu 22.04
Rocky Linux 8.10 & 9.3
Windows 11 Pro 22621

numpy
pandas
cupy
cuda-version==12.8
astropy
seaborn
scikit-image
scikit-spatial
pytest
pytest-order
matplotlib==3.8.4
ujson
zarr
pycudadecon
dphtools
tifffile==2023.9.18
imagecodecs==2023.9.18
nvitop
pycuda
pytest
tqdm
cachetools
line_profiler_pycharm

Caution

NVIDIA GPU with a driver release 545 or later, and CUDA 12.8.

Clone repository to your host system

git clone --recurse-submodules https://github.com/cell-observatory/beads_simulator.git

To later update to the latest, greatest

git pull --recurse-submodules

Create conda environment

conda/mamba create --name beads --file requirements.txt

Or use pip install -r requirements.txt

Running the simulator

Activate conda environment

conda activate beads

Features

Wavefront simulation
Fourier embedding
PSF dataset generator
Beads dataset generator
Multimodal beads dataset generator

Wavefront simulation

Simulation of ideal and aberrated wavefronts where the amplitudes of the zernike modes are drawn from a given distribution:
- Single
- Bimodal
- Multinomial
- Powerlaw
- Dirichlet

Tip

For more options, please refer to wavefront.py

Fourier embedding

Tip

For more options, please refer to embedding.py

Aberrated PSF

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_random_aberrated_psf

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_random_aberrated_psf Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/_home_thayer_Github_beads_simulator_lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
PASSED
=============================================== 1 passed, 8 deselected, 1 warning in 7.68s ================================================

LLS defocused PSF

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_random_defocused_psf

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_random_defocused_psf Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/_home_thayer_Github_beads_simulator_lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
PASSED

=============================================== 1 passed, 8 deselected, 1 warning in 7.68s ================================================

Aberrated and LLS defocused PSF

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_random_aberrated_defocused_psf

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_random_aberrated_defocused_psf Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/_home_thayer_Github_beads_simulator_lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
PASSED
=============================================== 1 passed, 8 deselected, 1 warning in 7.71s ================================================

PSF dataset generator

Tip

For more options, please refer to psf_dataset.py

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_psf_dataset

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_psf_dataset Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/_home_thayer_Github_beads_simulator_lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:03<00:00,  2.83it/s]
PASSED
===================================================== 1 passed, 8 deselected in 5.19s =====================================================

Tip

For more options, please refer to psf_dataset.py --help

usage: psf_dataset.py [-h] [--filename FILENAME] [--outdir OUTDIR] [--emb] [--iters ITERS] [--kernels] [--noise] [--normalize] [--x_voxel_size X_VOXEL_SIZE] [--y_voxel_size Y_VOXEL_SIZE] [--z_voxel_size Z_VOXEL_SIZE] [--input_shape INPUT_SHAPE] [--modes MODES] [--min_photons MIN_PHOTONS] [--max_photons MAX_PHOTONS] [--psf_type PSF_TYPE] [--dist DIST] [--mode_dist MODE_DIST] [--gamma GAMMA] [--signed] [--rotate] [--min_amplitude MIN_AMPLITUDE]
                      [--max_amplitude MAX_AMPLITUDE] [--min_lls_defocus_offset MIN_LLS_DEFOCUS_OFFSET] [--max_lls_defocus_offset MAX_LLS_DEFOCUS_OFFSET] [--refractive_index REFRACTIVE_INDEX] [--na_detection NA_DETECTION] [--lam_detection LAM_DETECTION] [--cpu_workers CPU_WORKERS] [--use_theoretical_widefield_simulator] [--skip_remove_background]

options:
  -h, --help            show this help message and exit
  --filename FILENAME
  --outdir OUTDIR
  --emb                 toggle to save fourier embeddings only
  --iters ITERS         number of samples (Default: `10`)
  --kernels             toggle to save raw kernels
  --noise               toggle to add random background and shot noise to the generated PSFs
  --normalize           toggle to scale the generated PSFs to 1.0
  --x_voxel_size X_VOXEL_SIZE
                        lateral voxel size in microns for X (Default: `0.125`)
  --y_voxel_size Y_VOXEL_SIZE
                        lateral voxel size in microns for Y (Default: `0.125`)
  --z_voxel_size Z_VOXEL_SIZE
                        axial voxel size in microns for Z (Default: `0.2`)
  --input_shape INPUT_SHAPE
                        PSF input shape (Default: `64`)
  --modes MODES         number of modes to describe aberration (Default: `55`)
  --min_photons MIN_PHOTONS
                        minimum photons for training samples (Default: `5000`)
  --max_photons MAX_PHOTONS
                        maximum photons for training samples (Default: `10000`)
  --psf_type PSF_TYPE   widefield, 2photon, confocal, or a path to an LLS excitation profile  (Default: `../lattice/YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat`)
  --dist DIST           distribution of the zernike amplitudes (Default: `single`)
  --mode_dist MODE_DIST
                        distribution of the zernike modes (Default: `pyramid`)
  --gamma GAMMA         exponent for the powerlaw distribution (Default: `0.75`)
  --signed              optional flag to generate a symmetric (pos/neg) semi-distributions for the given range of amplitudes
  --rotate              optional flag to introduce a random radial rotation to each zernike mode
  --min_amplitude MIN_AMPLITUDE
                        min amplitude for the zernike coefficients (Default: `0`)
  --max_amplitude MAX_AMPLITUDE
                        max amplitude for the zernike coefficients (Default: `0.25`)
  --min_lls_defocus_offset MIN_LLS_DEFOCUS_OFFSET
                        min value for the offset between the excitation and detection focal plan (microns) (Default: `0`)
  --max_lls_defocus_offset MAX_LLS_DEFOCUS_OFFSET
                        max value for the offset between the excitation and detection focal plan (microns) (Default: `0`)
  --refractive_index REFRACTIVE_INDEX
                        the quotient of the speed of light as it passes through two media (Default: `1.33`)
  --na_detection NA_DETECTION
                        Numerical aperture (Default: `1.0`)
  --lam_detection LAM_DETECTION
                        wavelength in microns (Default: `0.51`)
  --cpu_workers CPU_WORKERS
                        number of CPU cores to use (Default: `-1`)
  --use_theoretical_widefield_simulator
                        optional toggle to use an experimental complex pupil to estimate amplitude attenuation (cosine factor)
  --skip_remove_background
                        optional toggle to skip preprocessing input data using the DoG filter

Beads dataset generator

Synthatic samples with 1 up to $n$ beads randomly placed in a given FOV

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_multipoint_dataset

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_multipoint_dataset Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/_home_thayer_Github_beads_simulator_lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:14<00:00,  1.48s/it]
PASSED
=============================================== 1 passed, 8 deselected, 1 warning in 16.47s ===============================================

Tip

For more options, please refer to multipoint_dataset.py

usage: multipoint_dataset.py [-h] [--filename FILENAME] [--npoints NPOINTS] [--outdir OUTDIR] [--emb] [--embedding_option EMBEDDING_OPTION] [--iters ITERS] [--kernels] [--noise] [--normalize] [--x_voxel_size X_VOXEL_SIZE] [--y_voxel_size Y_VOXEL_SIZE] [--z_voxel_size Z_VOXEL_SIZE] [--input_shape INPUT_SHAPE] [--random_crop RANDOM_CROP] [--modes MODES] [--min_photons MIN_PHOTONS] [--max_photons MAX_PHOTONS] [--psf_type PSF_TYPE] [--dist DIST]
                             [--mode_dist MODE_DIST] [--gamma GAMMA] [--signed] [--rotate] [--randomize_object_size] [--min_amplitude MIN_AMPLITUDE] [--max_amplitude MAX_AMPLITUDE] [--min_lls_defocus_offset MIN_LLS_DEFOCUS_OFFSET] [--max_lls_defocus_offset MAX_LLS_DEFOCUS_OFFSET] [--refractive_index REFRACTIVE_INDEX] [--na_detection NA_DETECTION] [--fill_radius FILL_RADIUS] [--object_size OBJECT_SIZE] [--uniform_background UNIFORM_BACKGROUND]
                             [--lam_detection LAM_DETECTION] [--alpha_val ALPHA_VAL] [--phi_val PHI_VAL] [--cpu_workers CPU_WORKERS] [--override] [--plot] [--use_theoretical_widefield_simulator] [--skip_remove_background]

options:
  -h, --help            show this help message and exit
  --filename FILENAME
  --npoints NPOINTS
  --outdir OUTDIR
  --emb                 toggle to save fourier embeddings only
  --embedding_option EMBEDDING_OPTION
                        type of embedding to use: ["spatial_planes", "principle_planes", "rotary_slices", "spatial_quadrants"] (Default: `['spatial_planes']`)
  --iters ITERS         number of samples (Default: `10`)
  --kernels             toggle to save raw kernels
  --noise               toggle to add random background and shot noise to the generated PSFs
  --normalize           toggle to scale the generated PSFs to 1.0
  --x_voxel_size X_VOXEL_SIZE
                        lateral voxel size in microns for X (Default: `0.125`)
  --y_voxel_size Y_VOXEL_SIZE
                        lateral voxel size in microns for Y (Default: `0.125`)
  --z_voxel_size Z_VOXEL_SIZE
                        axial voxel size in microns for Z (Default: `0.2`)
  --input_shape INPUT_SHAPE
                        PSF input shape (Default: `64`)
  --random_crop RANDOM_CROP
  --modes MODES         number of modes to describe aberration (Default: `55`)
  --min_photons MIN_PHOTONS
                        minimum photons for training samples (Default: `5000`)
  --max_photons MAX_PHOTONS
                        maximum photons for training samples (Default: `10000`)
  --psf_type PSF_TYPE   widefield, 2photon, confocal, or a path to an LLS excitation profile (Default: `['../lattice/YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat']`)
  --dist DIST           distribution of the zernike amplitudes (Default: `single`)
  --mode_dist MODE_DIST
                        distribution of the zernike modes (Default: `pyramid`)
  --gamma GAMMA         exponent for the powerlaw distribution (Default: `0.75`)
  --signed              optional flag to generate a symmetric (pos/neg) semi-distributions for the given range of amplitudes
  --rotate              optional flag to introduce a random radial rotation to each zernike mode
  --randomize_object_size
                        optional flag to randomize voxel size during training
  --min_amplitude MIN_AMPLITUDE
                        min amplitude for the zernike coefficients (Default: `0`)
  --max_amplitude MAX_AMPLITUDE
                        max amplitude for the zernike coefficients (Default: `0.25`)
  --min_lls_defocus_offset MIN_LLS_DEFOCUS_OFFSET
                        min value for the offset between the excitation and detection focal plan (microns) (Default: `0`)
  --max_lls_defocus_offset MAX_LLS_DEFOCUS_OFFSET
                        max value for the offset between the excitation and detection focal plan (microns) (Default: `0`)
  --refractive_index REFRACTIVE_INDEX
                        the quotient of the speed of light as it passes through two media (Default: `1.33`)
  --na_detection NA_DETECTION
                        Numerical aperture (Default: `1.0`)
  --fill_radius FILL_RADIUS
                        Fractional cylinder radius (0-1) that defines where a bead may be placed in X Y Z. (Default: `0.0`)
  --object_size OBJECT_SIZE
                        optional bead size (Default: 0 for diffraction-limited beads, -1 for beads with random sizes) (Default: `0.0`)
  --uniform_background UNIFORM_BACKGROUND
                        optional uniform background value (Default: `0`)
  --lam_detection LAM_DETECTION
                        wavelength in microns (Default: `0.51`)
  --alpha_val ALPHA_VAL
                        values to use for the `alpha` embedding [options: real, abs] (Default: `abs`)
  --phi_val PHI_VAL     values to use for the `phi` embedding [options: angle, imag, abs] (Default: `angle`)
  --cpu_workers CPU_WORKERS
                        number of CPU cores to use (Default: `-1`)
  --override            optional toggle to override existing data
  --plot                optional toggle to plot preprocessing
  --use_theoretical_widefield_simulator
                        optional toggle to use an experimental complex pupil to estimate amplitude attenuation (cosine factor)
  --skip_remove_background
                        optional toggle to skip preprocessing input data using the DoG filter

Multimodal beads dataset generator

Synthatic samples with 1 up to $n$ beads randomly placed in a given FOV

Note

Supported PSFs (synthatic.py)

Lattice light sheets
Widefield
2photon
Confocal

pytest -s -v --disable-pytest-warnings --color=yes tests/test_datasets.py -k test_multimodal_dataset

=========================================================== test session starts ===========================================================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /home/thayer/miniforge3/envs/beads/bin/python3.12
cachedir: .pytest_cache
rootdir: /home/thayer/Github/beads_simulator
plugins: order-1.3.0
collected 9 items / 8 deselected / 1 selected

tests/test_datasets.py::test_multimodal_dataset Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_YuMB_NAlattice0p35_NAAnnulusMax0p40_NAsigma0p1.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_Gaussian_NAexc0p21_NAsigma0p21_annulus0p4-0p2_crop0p1_FWHM51p0.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_Gaussian_NAexc0p21_NAsigma0p21_annulus0p4-0p2_crop0p1_FWHM51p0.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_MBSq_NAexc0p30_annulus0p375-0p225_FWHM48p5.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_MBSq_NAexc0p30_annulus0p375-0p225_FWHM48p5.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_Sinc_by_lateral_SW_NAexc0p32_NAsigma5p0_annulus0p4-0p2_realSLM_FWHM51p5.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_Sinc_by_lateral_SW_NAexc0p32_NAsigma5p0_annulus0p4-0p2_realSLM_FWHM51p5.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_v2Hex_NAexc0p50_NAsigma0p075_annulus0p60-0p40_FWHM53p0.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_v2Hex_NAexc0p50_NAsigma0p075_annulus0p60-0p40_FWHM53p0.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_v2HexRect_NAexc0p50_NAsigma0p15_annulus0p60-0p40_FWHM_56p0.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_v2HexRect_NAexc0p50_NAsigma0p15_annulus0p60-0p40_FWHM_56p0.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_ACHex_NAexc0p40_NAsigma0p075_annulus0p6-0p2_crop0p1_FWHM52p0.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_ACHex_NAexc0p40_NAsigma0p075_annulus0p6-0p2_crop0p1_FWHM52p0.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_MBHex_NAexc0p43_annulus0p47_0p40_crop0p08_FWHM48p0.mat_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/.._lattice_MBHex_NAexc0p43_annulus0p47_0p40_crop0p08_FWHM48p0.mat_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/widefield_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/widefield_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/2photon_shape_64-64-64_lam_0.92_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/2photon_shape_128-128-128_lam_0.92_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/confocal_shape_64-64-64_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
Loading cached SyntheticPSF instance from /home/thayer/Github/beads_simulator/SyntheticPSFCache/confocal_shape_128-128-128_lam_0.51_na_1.0_ri_1.33_x_0.097_y_0.097_z_0.2_twd_simulator_False
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [04:48<00:00, 28.83s/it]
PASSED

========================================= 1 passed, 8 deselected, 1 warning in 290.55s (0:04:50) ==========================================

BibTeX

@article{alshaabi2025fourier,
  title={Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens},
  author={Thayer Alshaabi and Daniel E. Milkie and Gaoxiang Liu and Cyna Shirazinejad and Jason L. Hong and Kemal Achour and Frederik Görlitz and Ana Milunovic-Jevtic and Cat Simmons and Ibrahim S. Abuzahriyeh and Erin Hong and Samara Erin Williams and Nathanael Harrison and Evan Huang and Eun Seok Bae and Alison N. Killilea and David G. Drubin and Ian A. Swinburne and Srigokul Upadhyayula and Eric Betzig},
  journal={arXiv preprint arXiv:2503.12593},
  year={2025},
  url={https://arxiv.org/abs/2503.12593},
}

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

Apache License 2.0

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
lattice		lattice
src		src
tests		tests
.gitignore		.gitignore
.gitmodules		.gitmodules
LICENSE		LICENSE
README.md		README.md
requirements.txt		requirements.txt

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Beads simulator for AOViFT

Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens

¹HHMI, ²UC Berkeley, ³Lawrence Berkeley National Laboratory, ⁴Chan Zuckerberg Biohub, ⁵Helen Wills Neuroscience Institute

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Clone repository to your host system

Create conda environment

Running the simulator

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Wavefront simulation

Fourier embedding

Aberrated PSF

LLS defocused PSF

Aberrated and LLS defocused PSF

PSF dataset generator

Beads dataset generator

Multimodal beads dataset generator

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cell-observatory/beads_simulator

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Beads simulator for AOViFT

Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens

1HHMI, 2UC Berkeley, 3Lawrence Berkeley National Laboratory, 4Chan Zuckerberg Biohub, 5Helen Wills Neuroscience Institute

Installation

Dependencies

Clone repository to your host system

Create conda environment

Running the simulator

Features

Wavefront simulation

Fourier embedding

Aberrated PSF

LLS defocused PSF

Aberrated and LLS defocused PSF

PSF dataset generator

Beads dataset generator

Multimodal beads dataset generator

BibTeX

License

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¹HHMI, ²UC Berkeley, ³Lawrence Berkeley National Laboratory, ⁴Chan Zuckerberg Biohub, ⁵Helen Wills Neuroscience Institute

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