├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── docker ├── Dockerfile ├── Dockerfile.devel └── Dockerfile.gpu ├── docs └── images │ ├── astro.png │ └── neuron.png ├── java ├── .gitignore └── flowdec │ ├── .gitignore │ ├── pom.xml │ └── src │ ├── main │ └── java │ │ └── org │ │ └── hammerlab │ │ └── flowdec │ │ ├── Flowdec.java │ │ ├── FlowdecData.java │ │ ├── FlowdecTask.java │ │ ├── IJUtils.java │ │ └── examples │ │ └── MultiGPUExample.java │ └── test │ └── java │ └── org │ └── hammerlab │ └── flowdec │ └── FlowdecTest.java ├── python ├── examples │ ├── notebooks │ │ ├── Algorithm Graph Export.ipynb │ │ ├── Astronaut - Ringing Artifacts.ipynb │ │ ├── CElegans - Multiple Channel Example.ipynb │ │ ├── DeconvolutionLab2 - Benchmarking.ipynb │ │ ├── Fluorescent Bead - Synthetic Deconvolution.ipynb │ │ ├── Hollow Bars - Benchmarking.ipynb │ │ ├── Hollow Bars - Synthetic Deconvolution.ipynb │ │ ├── Monitoring Iterations.ipynb │ │ ├── Neuron - 3D Deconvolution.ipynb │ │ ├── Point Source - Synthetic Deconvolution.ipynb │ │ ├── Tile-by-tile deconvolution using dask.ipynb │ │ └── Unit Test Generation.ipynb │ └── scripts │ │ ├── deconvolution.py │ │ └── graph_exports.py ├── flowdec │ ├── __init__.py │ ├── cmd │ │ ├── __init__.py │ │ └── deconvolution.py │ ├── data.py │ ├── datasets │ │ ├── __init__.py │ │ ├── bars-25pct │ │ │ ├── actual.tif │ │ │ ├── data.tif │ │ │ └── kernel.tif │ │ ├── bead-25pct │ │ │ ├── data.tif │ │ │ └── kernel.tif │ │ ├── neuron-25pct │ │ │ └── data.tif │ │ └── psfs │ │ │ └── psfgen1.tif │ ├── exec.py │ ├── fft_pad_rainbow.py │ ├── fft_utils_np.py │ ├── fft_utils_test.py │ ├── fft_utils_tf.py │ ├── nb │ │ ├── __init__.py │ │ ├── logging.py │ │ └── utils.py │ ├── psf.py │ ├── psf_test.py │ ├── restoration.py │ ├── restoration_test.py │ ├── test_utils.py │ ├── tf_ops.py │ ├── tf_ops_test.py │ └── validation.py ├── requirements.txt ├── setup.py ├── test-requirements.txt ├── tests │ └── smoketest.sh ├── tox.ini └── validation │ ├── deconvolution │ ├── results │ │ ├── bars-crop.ipynb │ │ ├── bars-samp.ipynb │ │ ├── bead-samp.ipynb │ │ ├── celegans-dapi-crop.ipynb │ │ ├── microtubules-crop.ipynb │ │ └── microtubules-samp.ipynb │ ├── template.ipynb │ └── validation.ipynb │ └── psfgeneration │ ├── results │ ├── blue-light.ipynb │ ├── green-light.ipynb │ ├── hi-zres.ipynb │ ├── large-xy.ipynb │ ├── large-z.ipynb │ ├── low-zres.ipynb │ ├── particle-pos-n1um.ipynb │ ├── particle-pos-p1um.ipynb │ └── red-light.ipynb │ ├── template.ipynb │ ├── utils.py │ └── validation.ipynb └── tensorflow ├── richardsonlucy-complex-1d └── saved_model.pb ├── richardsonlucy-complex-2d └── saved_model.pb └── richardsonlucy-complex-3d └── saved_model.pb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hammerlab/flowdec/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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