MANIFEST.in
README.rst
REQUIREMENTS.txt
setup.py
sptx_format/__init__.py
sptx_format/cli.py
sptx_format/test_codebook.py
sptx_format/test_experiment.py
sptx_format/test_field_of_view.py
sptx_format/test_fov_manifest.py
sptx_format/test_fuzz.py
sptx_format/util.py
sptx_format/validate_sptx.py
sptx_format/examples/codebook/codebook.json
sptx_format/examples/codebook/codebook_diagonal.json
sptx_format/examples/codebook/codebook_diagonal_inferred_value.json
sptx_format/examples/experiment/dartfish_experiment.json
sptx_format/examples/experiment/experiment.json
sptx_format/examples/experiment/no_fov_manifest.json
sptx_format/examples/field_of_view/dartfish_field_of_view.json
sptx_format/examples/field_of_view/dartfish_nuclei.json
sptx_format/examples/field_of_view/field_of_view.json
sptx_format/examples/fov_manifest/fov_manifest.json
sptx_format/schema/experiment.json
sptx_format/schema/extras.json
sptx_format/schema/fov_manifest.json
sptx_format/schema/version.json
sptx_format/schema/codebook/codebook.json
sptx_format/schema/codebook/codeword.json
sptx_format/schema/field_of_view/field_of_view.json
sptx_format/schema/field_of_view/tiles/coordinates.json
sptx_format/schema/field_of_view/tiles/indices.json
sptx_format/schema/field_of_view/tiles/tiles.json
starfish/__init__.py
starfish/__main__.py
starfish/errors.py
starfish/starfish.py
starfish/types.py
starfish.egg-info/PKG-INFO
starfish.egg-info/SOURCES.txt
starfish.egg-info/dependency_links.txt
starfish.egg-info/entry_points.txt
starfish.egg-info/requires.txt
starfish.egg-info/top_level.txt
starfish/codebook/__init__.py
starfish/codebook/_format.py
starfish/codebook/codebook.py
starfish/data/__init__.py
starfish/experiment/__init__.py
starfish/experiment/experiment.py
starfish/experiment/version.py
starfish/experiment/builder/__init__.py
starfish/experiment/builder/cli.py
starfish/experiment/builder/defaultproviders.py
starfish/experiment/builder/orderediterator.py
starfish/experiment/builder/providers.py
starfish/expression_matrix/__init__.py
starfish/expression_matrix/expression_matrix.py
starfish/image/__init__.py
starfish/image/_filter/__init__.py
starfish/image/_filter/_base.py
starfish/image/_filter/bandpass.py
starfish/image/_filter/clip.py
starfish/image/_filter/gaussian_high_pass.py
starfish/image/_filter/gaussian_low_pass.py
starfish/image/_filter/laplace.py
starfish/image/_filter/max_proj.py
starfish/image/_filter/mean_high_pass.py
starfish/image/_filter/richardson_lucy_deconvolution.py
starfish/image/_filter/scale_by_percentile.py
starfish/image/_filter/util.py
starfish/image/_filter/white_tophat.py
starfish/image/_filter/zero_by_channel_magnitude.py
starfish/image/_registration/__init__.py
starfish/image/_registration/_base.py
starfish/image/_registration/fourier_shift.py
starfish/image/_segmentation/__init__.py
starfish/image/_segmentation/_base.py
starfish/image/_segmentation/watershed.py
starfish/imagestack/__init__.py
starfish/imagestack/_mp_dataarray.py
starfish/imagestack/dataorder.py
starfish/imagestack/imagestack.py
starfish/imagestack/indexing_utils.py
starfish/imagestack/physical_coordinate_calculator.py
starfish/intensity_table/__init__.py
starfish/intensity_table/concatenate.py
starfish/intensity_table/intensity_table.py
starfish/intensity_table/intensity_table_coordinates.py
starfish/multiprocessing/__init__.py
starfish/multiprocessing/shmem.py
starfish/pipeline/__init__.py
starfish/pipeline/algorithmbase.py
starfish/pipeline/pipelinecomponent.py
starfish/plot/__init__.py
starfish/plot/copy_number_comparison.py
starfish/plot/decoded_spots.py
starfish/plot/histogram.py
starfish/plot/style.py
starfish/plot/util.py
starfish/spots/__init__.py
starfish/spots/_decoder/__init__.py
starfish/spots/_decoder/_base.py
starfish/spots/_decoder/per_round_max_channel_decoder.py
starfish/spots/_detector/__init__.py
starfish/spots/_detector/_base.py
starfish/spots/_detector/blob.py
starfish/spots/_detector/combine_adjacent_features.py
starfish/spots/_detector/detect.py
starfish/spots/_detector/local_max_peak_finder.py
starfish/spots/_detector/pixel_spot_detector.py
starfish/spots/_detector/trackpy_local_max_peak_finder.py
starfish/spots/_target_assignment/__init__.py
starfish/spots/_target_assignment/_base.py
starfish/spots/_target_assignment/label.py
starfish/test/__init__.py
starfish/test/dataset_fixtures.py
starfish/test/test_config.py
starfish/test/test_multiprocessing.py
starfish/test/test_stack_intensity_table_reshaping.py
starfish/test/test_synthetic_data.py
starfish/test/test_utils.py
starfish/test/test_version.py
starfish/test/codebook/__init__.py
starfish/test/codebook/test_approximate_nearest_code.py
starfish/test/codebook/test_code_length.py
starfish/test/codebook/test_from_code_array.py
starfish/test/codebook/test_metric_decode.py
starfish/test/codebook/test_per_round_max_decode.py
starfish/test/codebook/test_synthetic_one_hot_codebook.py
starfish/test/expression_matrix/__init__.py
starfish/test/expression_matrix/test_serialization.py
starfish/test/full_pipelines/__init__.py
starfish/test/full_pipelines/api/__init__.py
starfish/test/full_pipelines/api/test_allen_smFISH.py
starfish/test/full_pipelines/api/test_dartfish.py
starfish/test/full_pipelines/api/test_iss_api.py
starfish/test/full_pipelines/api/test_iss_doc_pipeline.py
starfish/test/full_pipelines/api/test_merfish.py
starfish/test/full_pipelines/cli/__init__.py
starfish/test/full_pipelines/cli/_base_cli_test.py
starfish/test/full_pipelines/cli/test_allen_smFISH_cli.py
starfish/test/full_pipelines/cli/test_build.py
starfish/test/full_pipelines/cli/test_dartfish_cli.py
starfish/test/full_pipelines/cli/test_iss.py
starfish/test/full_pipelines/cli/test_merfish_cli.py
starfish/test/full_pipelines/cli/test_profiler.py
starfish/test/full_pipelines/cli/test_validate.py
starfish/test/image/__init__.py
starfish/test/image/test_apply.py
starfish/test/image/test_imagestack.py
starfish/test/image/test_imagestack_coordinates.py
starfish/test/image/test_imagestack_index.py
starfish/test/image/test_imagestack_metadata.py
starfish/test/image/test_physical_coordinate_calculator.py
starfish/test/image/test_slicedimage_dtype.py
starfish/test/image/filter/__init__.py
starfish/test/image/filter/test_api_contract.py
starfish/test/image/filter/test_zero_by_channel_magnitude.py
starfish/test/intensity_table/__init__.py
starfish/test/intensity_table/test_concatenate.py
starfish/test/intensity_table/test_empty_intensity_table.py
starfish/test/intensity_table/test_from_imagestack.py
starfish/test/intensity_table/test_from_spot_data.py
starfish/test/intensity_table/test_intensity_table_coords.py
starfish/test/intensity_table/test_intensity_table_serialization.py
starfish/test/intensity_table/test_synthetic_intensities.py
starfish/test/intensity_table/test_to_expression_matrix.py
starfish/test/intensity_table/test_to_mermaid.py
starfish/test/pipeline/__init__.py
starfish/test/pipeline/test_filter.py
starfish/test/pipeline/test_white_tophat.py
starfish/test/spots/__init__.py
starfish/test/spots/detector/__init__.py
starfish/test/spots/detector/test_spot_detection.py
starfish/test/spots/detector/pixel_spot_detector/__init__.py
starfish/test/spots/detector/pixel_spot_detector/combine_adjacent_features/__init__.py
starfish/test/spots/detector/pixel_spot_detector/combine_adjacent_features/test_calculate_mean_pixel_traces.py
starfish/test/spots/detector/pixel_spot_detector/combine_adjacent_features/test_create_spot_attributes.py
starfish/test/spots/detector/pixel_spot_detector/combine_adjacent_features/test_intensities_to_decoded_image.py
starfish/test/spots/detector/pixel_spot_detector/combine_adjacent_features/test_targets_map.py
starfish/test/spots/target_assignment/__init__.py
starfish/test/spots/util/__init__.py
starfish/test/spots/util/test_normalize_code_traces.py
starfish/types/__init__.py
starfish/types/_constants.py
starfish/types/_spot_attributes.py
starfish/types/_validated_table.py
starfish/util/__init__.py
starfish/util/_functools.py
starfish/util/argparse.py
starfish/util/clock.py
starfish/util/config.py
starfish/util/exec.py
starfish/util/synthesize.py
starfish/util/try_import.py