.gitignore
.pre-commit-config.yaml
LICENSE.txt
README.md
pyproject.toml
requirements.txt
setup.py
.github/workflows/pypi-release.yml
.github/workflows/test.yml
data/.gitignore
examples/correct_organoid.py
examples/correct_organoid_arr.py
examples/motion_correct_3d_flowreg3d_volRAFT_combined.py
examples/motion_correct_3d_test.py
examples/motion_correct_3d_volraft_test.py
img/bg.png
img/comparison.png
img/flowreglogo.png
notebooks/requirements_notebooks.txt
notebooks/synthetic_example.ipynb
src/flowreg3d/__init__.py
src/flowreg3d/_runtime.py
src/flowreg3d/_version.py
src/flowreg3d.egg-info/PKG-INFO
src/flowreg3d.egg-info/SOURCES.txt
src/flowreg3d.egg-info/dependency_links.txt
src/flowreg3d.egg-info/entry_points.txt
src/flowreg3d.egg-info/requires.txt
src/flowreg3d.egg-info/top_level.txt
src/flowreg3d/cli/__init__.py
src/flowreg3d/cli/concat_tiffs.py
src/flowreg3d/cli/main.py
src/flowreg3d/cli/tiff_reshape.py
src/flowreg3d/core/__init__.py
src/flowreg3d/core/level_solver_3d.py
src/flowreg3d/core/optical_flow_3d.py
src/flowreg3d/core/torch/__init__.py
src/flowreg3d/core/torch/level_solver_3d.py
src/flowreg3d/core/torch/optical_flow_3d.py
src/flowreg3d/motion_correction/OF_options_3D.py
src/flowreg3d/motion_correction/__init__.py
src/flowreg3d/motion_correction/compensate_arr_3D.py
src/flowreg3d/motion_correction/compensate_recording_3D.py
src/flowreg3d/motion_correction/parallelization/__init__.py
src/flowreg3d/motion_correction/parallelization/base_3d.py
src/flowreg3d/motion_correction/parallelization/multiprocessing_3d.py
src/flowreg3d/motion_correction/parallelization/sequential_3d.py
src/flowreg3d/motion_correction/parallelization/threading_3d.py
src/flowreg3d/motion_generation/__init__.py
src/flowreg3d/motion_generation/motion_generators.py
src/flowreg3d/util/__init__.py
src/flowreg3d/util/image_processing_3D.py
src/flowreg3d/util/random.py
src/flowreg3d/util/resize_util_3D.py
src/flowreg3d/util/xcorr_prealignment.py
src/flowreg3d/util/io/__init__.py
src/flowreg3d/util/io/_arr_3d.py
src/flowreg3d/util/io/_base.py
src/flowreg3d/util/io/_base_3d.py
src/flowreg3d/util/io/_ds_io_3d.py
src/flowreg3d/util/io/_scanimage.py
src/flowreg3d/util/io/factory.py
src/flowreg3d/util/io/hdf5_3d.py
src/flowreg3d/util/io/mat_3d.py
src/flowreg3d/util/io/multifile_wrappers_3d.py
src/flowreg3d/util/io/tiff.py
src/flowreg3d/util/io/tiff_3d.py
src/flowreg3d/util/torch/__init__.py
src/flowreg3d/util/torch/image_processing_3D.py
src/flowreg3d/util/torch/resize_util_3D.py
tests/README.md
tests/__init__.py
tests/conftest.py
tests/fixtures_3d.py
tests/cli/__init__.py
tests/cli/test_concat_tiffs.py
tests/cli/test_main.py
tests/cli/test_tiff_reshape.py
tests/core/__init__.py
tests/motion_correction/__init__.py
tests/motion_correction/test_OF_options_3D.py
tests/motion_correction/test_compensate_arr_3D.py
tests/motion_correction/test_compensate_recording_3D.py
tests/motion_correction/test_parallelization.py
tests/util/__init__.py
tests/util/test_xcorr_prealignment.py
tests/util/torch/__init__.py
tests/util/torch/test_image_processing_3D.py
tests/util/torch/test_resize_util_3D.py