├── .github └── workflows │ ├── build-readme-pypi.yml │ ├── ci.yml │ └── docs.yml ├── .gitignore ├── .pylintrc ├── .vscode └── settings.json ├── .zenodo.json ├── CITATION.cff ├── LICENSE ├── README-pypi.md ├── README.md ├── assets ├── DeeepTrack2-logo.svg ├── DeepTrack2-logo.png ├── MPT-packed.gif ├── MPT-qdots_1.png ├── SPT-ideal.gif ├── SPT-noisy.gif ├── Tracing.gif └── strip_gh_only_blocks.py ├── deeptrack ├── __init__.py ├── aberrations.py ├── augmentations.py ├── backend │ ├── __init__.py │ ├── _config.py │ ├── array_api_compat_ext │ │ ├── __init__.py │ │ └── torch │ │ │ ├── __init__.py │ │ │ └── random.py │ ├── core.py │ ├── mie.py │ ├── pint_definition.py │ ├── polynomials.py │ └── units.py ├── deeplay │ └── __init__.py ├── elementwise.py ├── extras │ ├── __init__.py │ └── radialcenter.py ├── features.py ├── holography.py ├── image.py ├── math.py ├── noises.py ├── optics.py ├── properties.py ├── pytorch │ ├── __init__.py │ ├── data.py │ └── features.py ├── scatterers.py ├── sequences.py ├── sources │ ├── __init__.py │ ├── base.py │ ├── folder.py │ └── rng.py ├── statistics.py ├── tests │ ├── __init__.py │ ├── backend │ │ ├── __init__.py │ │ ├── test__config.py │ │ ├── test_core.py │ │ ├── test_mie.py │ │ ├── test_polynomials.py │ │ └── test_units.py │ ├── extras │ │ ├── __init__.py │ │ └── test_radialcenter.py │ ├── sources │ │ ├── __init__.py │ │ ├── test_base.py │ │ └── test_folder.py │ ├── test_aberrations.py │ ├── test_augmentations.py │ ├── test_dlcc.py │ ├── test_elementwise.py │ ├── test_features.py │ ├── test_holography.py │ ├── test_image.py │ ├── test_math.py │ ├── test_noises.py │ ├── test_optics.py │ ├── test_properties.py │ ├── test_scatterers.py │ ├── test_sequences.py │ ├── test_statistics.py │ └── test_utils.py ├── types.py └── utils.py ├── package.json ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py └── tutorials ├── 1-getting-started ├── DTGS101_intro.ipynb ├── DTGS106_particle_image_modalities.ipynb ├── DTGS111_datafiles.ipynb ├── DTGS121_tracking_particle_cnn.ipynb ├── DTGS126_characterizing_aberrations_cnn.ipynb ├── DTGS127_characterizing_aberrations_optuna.ipynb ├── DTGS131_tracking_multiple_particles_unet.ipynb ├── DTGS141_distinguishing_particles_in_brightfield.ipynb ├── DTGS151_unsupervised_object_detection_with_lodestar.ipynb ├── DTGS161_torch_fitting.ipynb ├── DTGS171A_custom_scatterers.ipynb └── DTGS171B_custom_scatterers_bacteria.ipynb ├── 2-examples ├── DTEx203_particle_sizing.ipynb ├── DTEx205_inline_holography_3d_tracking.ipynb ├── DTEx206_cell_counting.ipynb ├── DTEx207_GAN_image_generation.ipynb ├── DTEx211_MNIST.ipynb ├── DTEx212_single_particle_tracking.ipynb ├── DTEx213_multi_particle_tracking.ipynb ├── DTEx231A_LodeSTAR_autotracker_template.ipynb ├── DTEx231B_LodeSTAR_tracking_particles_of_various_shapes.ipynb ├── DTEx231C_LodeSTAR_measure_mass_experimental.ipynb ├── DTEx231D_LodeSTAR_track_BF-C2DL-HSC.ipynb ├── DTEx231E_LodeSTAR_track_Fluo-C2DL-Huh7.ipynb ├── DTEx231F_LodeSTAR_track_PhC-C2DL-PSC.ipynb ├── DTEx231G_LodeSTAR_track_plankton.ipynb ├── DTEx231H_LodeSTAR_track_3D_holography.ipynb ├── DTEx231I_LodeSTAR_measure_mass_simulated.ipynb ├── DTEx231J_LodeSTAR_measure_mass_cell.ipynb ├── DTEx241A_MAGIK_cell_migration_analysis.ipynb ├── DTEx241B_MAGIK_tracking_hela_cells.ipynb ├── assets │ ├── data.npy │ ├── overview.png │ └── plankton.npy └── readme_to_incorporate into MAGIK examples.md ├── 3-advanced-topics ├── DTAT301_features.ipynb ├── DTAT306_properties.ipynb ├── DTAT311_image.ipynb ├── DTAT321_scatterers.ipynb ├── DTAT323_optics.ipynb ├── DTAT324_holography.ipynb ├── DTAT325_aberrations.ipynb ├── DTAT327_noises.ipynb ├── DTAT329_augmentations.ipynb ├── DTAT341_sequences.ipynb ├── DTAT381_math.ipynb ├── DTAT383_utils.ipynb ├── DTAT385_statistics.ipynb ├── DTAT387_types.ipynb ├── DTAT389_elementwise.ipynb ├── DTAT391A_sources.base.ipynb ├── DTAT391B_sources.folder.ipynb ├── DTAT391C_sources.rng.ipynb ├── DTAT393A_pytorch.features.ipynb ├── DTAT393B_pytorch.data.ipynb ├── DTAT395_extras.radialcenter.ipynb ├── DTAT399A_backend.core.ipynb ├── DTAT399B_backend.pint_definition.ipynb ├── DTAT399C_backend.units.ipynb ├── DTAT399D_backend.polynomials.ipynb ├── DTAT399E_backend.mie.ipynb └── DTAT399F_backend._config.ipynb ├── 4-developers ├── DTDV401_overview.ipynb ├── DTDV411_style.ipynb └── DTDV421_backends.ipynb └── test_notebooks.py /.github/workflows/build-readme-pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DeepTrackAI/DeepTrack2/HEAD/.github/workflows/build-readme-pypi.yml -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DeepTrackAI/DeepTrack2/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- 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