MANIFEST.in
README.rst
REQUIREMENTS.txt
setup.cfg
setup.py
versioneer.py
starfish/REQUIREMENTS-STRICT.txt
starfish/__init__.py
starfish/__main__.py
starfish/config.py
starfish/data.py
starfish/image.py
starfish/morphology.py
starfish/spots.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/core/__init__.py
starfish/core/_display.py
starfish/core/_version.py
starfish/core/compat.py
starfish/core/errors.py
starfish/core/starfish.py
starfish/core/codebook/__init__.py
starfish/core/codebook/_format.py
starfish/core/codebook/codebook.py
starfish/core/codebook/test/__init__.py
starfish/core/codebook/test/factories.py
starfish/core/codebook/test/test_approximate_nearest_code.py
starfish/core/codebook/test/test_code_length.py
starfish/core/codebook/test/test_from_code_array.py
starfish/core/codebook/test/test_metric_decode.py
starfish/core/codebook/test/test_normalize_code_traces.py
starfish/core/codebook/test/test_per_round_max_decode.py
starfish/core/codebook/test/test_synthetic_one_hot_codebook.py
starfish/core/codebook/test/test_to_json.py
starfish/core/config/__init__.py
starfish/core/config/test/__init__.py
starfish/core/config/test/test_config.py
starfish/core/experiment/__init__.py
starfish/core/experiment/experiment.py
starfish/core/experiment/version.py
starfish/core/experiment/builder/__init__.py
starfish/core/experiment/builder/defaultproviders.py
starfish/core/experiment/builder/inplace.py
starfish/core/experiment/builder/orderediterator.py
starfish/core/experiment/builder/providers.py
starfish/core/experiment/builder/structured_formatter.py
starfish/core/experiment/builder/test/__init__.py
starfish/core/experiment/builder/test/test_inplace.py
starfish/core/experiment/builder/test/test_orderediterator.py
starfish/core/experiment/builder/test/test_small_axis.py
starfish/core/experiment/builder/test/factories/__init__.py
starfish/core/experiment/builder/test/factories/all_purpose.py
starfish/core/experiment/builder/test/factories/unique_tiles.py
starfish/core/experiment/builder/test/structured_formatter/__init__.py
starfish/core/experiment/builder/test/structured_formatter/test_multiple_fov.py
starfish/core/experiment/builder/test/structured_formatter/test_single_fov.py
starfish/core/experiment/builder/test/structured_formatter/test_tilepath.py
starfish/core/experiment/builder/test/structured_formatter/util.py
starfish/core/experiment/test/__init__.py
starfish/core/experiment/test/test_experiment.py
starfish/core/experiment/test/test_version.py
starfish/core/expression_matrix/__init__.py
starfish/core/expression_matrix/concatenate.py
starfish/core/expression_matrix/expression_matrix.py
starfish/core/expression_matrix/test/__init__.py
starfish/core/expression_matrix/test/test_concatenate.py
starfish/core/expression_matrix/test/test_serialization.py
starfish/core/image/__init__.py
starfish/core/image/Filter/__init__.py
starfish/core/image/Filter/_base.py
starfish/core/image/Filter/bandpass.py
starfish/core/image/Filter/call_bases.py
starfish/core/image/Filter/clip.py
starfish/core/image/Filter/clip_percentile_to_zero.py
starfish/core/image/Filter/clip_value_to_zero.py
starfish/core/image/Filter/element_wise_mult.py
starfish/core/image/Filter/gaussian_high_pass.py
starfish/core/image/Filter/gaussian_low_pass.py
starfish/core/image/Filter/laplace.py
starfish/core/image/Filter/linear_unmixing.py
starfish/core/image/Filter/map.py
starfish/core/image/Filter/match_histograms.py
starfish/core/image/Filter/mean_high_pass.py
starfish/core/image/Filter/reduce.py
starfish/core/image/Filter/richardson_lucy_deconvolution.py
starfish/core/image/Filter/util.py
starfish/core/image/Filter/white_tophat.py
starfish/core/image/Filter/zero_by_channel_magnitude.py
starfish/core/image/Filter/test/__init__.py
starfish/core/image/Filter/test/test_api_contract.py
starfish/core/image/Filter/test/test_call_bases.py
starfish/core/image/Filter/test/test_filter.py
starfish/core/image/Filter/test/test_histogram_matching.py
starfish/core/image/Filter/test/test_linear_unmixing.py
starfish/core/image/Filter/test/test_map.py
starfish/core/image/Filter/test/test_reduce.py
starfish/core/image/Filter/test/test_white_tophat.py
starfish/core/image/Filter/test/test_zero_by_channel_magnitude.py
starfish/core/image/Segment/__init__.py
starfish/core/image/Segment/_base.py
starfish/core/image/Segment/watershed.py
starfish/core/image/_registration/__init__.py
starfish/core/image/_registration/_format.py
starfish/core/image/_registration/transforms_list.py
starfish/core/image/_registration/ApplyTransform/__init__.py
starfish/core/image/_registration/ApplyTransform/_base.py
starfish/core/image/_registration/ApplyTransform/warp.py
starfish/core/image/_registration/ApplyTransform/test/__init__.py
starfish/core/image/_registration/ApplyTransform/test/test_warp.py
starfish/core/image/_registration/LearnTransform/__init__.py
starfish/core/image/_registration/LearnTransform/_base.py
starfish/core/image/_registration/LearnTransform/translation.py
starfish/core/image/_registration/LearnTransform/test/__init__.py
starfish/core/image/_registration/LearnTransform/test/test_translation.py
starfish/core/image/_registration/test/__init__.py
starfish/core/image/_registration/test/test_transforms_list.py
starfish/core/imagestack/__init__.py
starfish/core/imagestack/dataorder.py
starfish/core/imagestack/imagestack.py
starfish/core/imagestack/indexing_utils.py
starfish/core/imagestack/physical_coordinates.py
starfish/core/imagestack/parser/__init__.py
starfish/core/imagestack/parser/_key.py
starfish/core/imagestack/parser/_tiledata.py
starfish/core/imagestack/parser/crop.py
starfish/core/imagestack/parser/numpy/__init__.py
starfish/core/imagestack/parser/tileset/__init__.py
starfish/core/imagestack/parser/tileset/_parser.py
starfish/core/imagestack/test/__init__.py
starfish/core/imagestack/test/imagestack_test_utils.py
starfish/core/imagestack/test/test_apply.py
starfish/core/imagestack/test/test_coordinates.py
starfish/core/imagestack/test/test_cropped_load.py
starfish/core/imagestack/test/test_export.py
starfish/core/imagestack/test/test_from_numpy_array.py
starfish/core/imagestack/test/test_index.py
starfish/core/imagestack/test/test_labeled_indices.py
starfish/core/imagestack/test/test_max_proj.py
starfish/core/imagestack/test/test_metadata.py
starfish/core/imagestack/test/test_physical_coordinate_calculator.py
starfish/core/imagestack/test/test_slice_ops.py
starfish/core/imagestack/test/test_slicedimage_dtype.py
starfish/core/imagestack/test/factories/__init__.py
starfish/core/imagestack/test/factories/all_purpose.py
starfish/core/imagestack/test/factories/from_codebook.py
starfish/core/imagestack/test/factories/synthetic_stack.py
starfish/core/imagestack/test/factories/unique_tiles.py
starfish/core/imagestack/test/factories/with_coords.py
starfish/core/intensity_table/__init__.py
starfish/core/intensity_table/concatenate.py
starfish/core/intensity_table/decoded_intensity_table.py
starfish/core/intensity_table/intensity_table.py
starfish/core/intensity_table/intensity_table_coordinates.py
starfish/core/intensity_table/overlap.py
starfish/core/intensity_table/test/__init__.py
starfish/core/intensity_table/test/factories.py
starfish/core/intensity_table/test/test_concatenate.py
starfish/core/intensity_table/test/test_empty_intensity_table.py
starfish/core/intensity_table/test/test_from_imagestack.py
starfish/core/intensity_table/test/test_from_spot_data.py
starfish/core/intensity_table/test/test_intensity_table_coords.py
starfish/core/intensity_table/test/test_intensity_table_serialization.py
starfish/core/intensity_table/test/test_overlap.py
starfish/core/intensity_table/test/test_stack_intensity_table_reshaping.py
starfish/core/intensity_table/test/test_synthetic_intensities.py
starfish/core/intensity_table/test/test_to_mermaid.py
starfish/core/morphology/__init__.py
starfish/core/morphology/util.py
starfish/core/morphology/Binarize/__init__.py
starfish/core/morphology/Binarize/_base.py
starfish/core/morphology/Binarize/threshold.py
starfish/core/morphology/Binarize/test/__init__.py
starfish/core/morphology/Binarize/test/test_threshold.py
starfish/core/morphology/Filter/__init__.py
starfish/core/morphology/Filter/_base.py
starfish/core/morphology/Filter/areafilter.py
starfish/core/morphology/Filter/map.py
starfish/core/morphology/Filter/min_distance_label.py
starfish/core/morphology/Filter/structural_label.py
starfish/core/morphology/Filter/test/__init__.py
starfish/core/morphology/Filter/test/test_areafilter.py
starfish/core/morphology/Filter/test/test_map.py
starfish/core/morphology/binary_mask/__init__.py
starfish/core/morphology/binary_mask/_io.py
starfish/core/morphology/binary_mask/binary_mask.py
starfish/core/morphology/binary_mask/expand.py
starfish/core/morphology/binary_mask/test/__init__.py
starfish/core/morphology/binary_mask/test/factories.py
starfish/core/morphology/binary_mask/test/test_binary_mask.py
starfish/core/morphology/binary_mask/test/test_expand.py
starfish/core/morphology/binary_mask/test/test_from_binary_arrays_and_ticks.py
starfish/core/morphology/binary_mask/test/test_from_label_array_and_ticks.py
starfish/core/morphology/label_image/__init__.py
starfish/core/morphology/label_image/label_image.py
starfish/core/morphology/label_image/test/__init__.py
starfish/core/morphology/label_image/test/test_label_image.py
starfish/core/pipeline/__init__.py
starfish/core/pipeline/algorithmbase.py
starfish/core/segmentation_mask/__init__.py
starfish/core/segmentation_mask/segmentation_mask.py
starfish/core/spacetx_format/__init__.py
starfish/core/spacetx_format/cli.py
starfish/core/spacetx_format/test_codebook.py
starfish/core/spacetx_format/test_coordinates.py
starfish/core/spacetx_format/test_experiment.py
starfish/core/spacetx_format/test_field_of_view.py
starfish/core/spacetx_format/test_fov_manifest.py
starfish/core/spacetx_format/test_fuzz.py
starfish/core/spacetx_format/util.py
starfish/core/spacetx_format/validate_sptx.py
starfish/core/spots/__init__.py
starfish/core/spots/AssignTargets/__init__.py
starfish/core/spots/AssignTargets/_base.py
starfish/core/spots/AssignTargets/label.py
starfish/core/spots/DecodeSpots/__init__.py
starfish/core/spots/DecodeSpots/_base.py
starfish/core/spots/DecodeSpots/metric_decoder.py
starfish/core/spots/DecodeSpots/per_round_max_channel_decoder.py
starfish/core/spots/DecodeSpots/simple_lookup_decoder.py
starfish/core/spots/DecodeSpots/trace_builders.py
starfish/core/spots/DecodeSpots/util.py
starfish/core/spots/DecodeSpots/test/__init__.py
starfish/core/spots/DecodeSpots/test/test_composite_codebook.py
starfish/core/spots/DecodeSpots/test/test_decoding_without_spots.py
starfish/core/spots/DecodeSpots/test/test_nearest_neighbor_trace_builder.py
starfish/core/spots/DecodeSpots/test/test_trace_builders.py
starfish/core/spots/DetectPixels/__init__.py
starfish/core/spots/DetectPixels/_base.py
starfish/core/spots/DetectPixels/combine_adjacent_features.py
starfish/core/spots/DetectPixels/pixel_spot_decoder.py
starfish/core/spots/DetectPixels/test/__init__.py
starfish/core/spots/DetectPixels/test/test_calculate_mean_pixel_traces.py
starfish/core/spots/DetectPixels/test/test_create_spot_attributes.py
starfish/core/spots/DetectPixels/test/test_intensities_to_decoded_image.py
starfish/core/spots/DetectPixels/test/test_targets_map.py
starfish/core/spots/FindSpots/__init__.py
starfish/core/spots/FindSpots/_base.py
starfish/core/spots/FindSpots/blob.py
starfish/core/spots/FindSpots/local_max_peak_finder.py
starfish/core/spots/FindSpots/spot_finding_utils.py
starfish/core/spots/FindSpots/trackpy_local_max_peak_finder.py
starfish/core/spots/FindSpots/test/__init__.py
starfish/core/spots/FindSpots/test/test_spot_detection.py
starfish/core/spots/FindSpots/test/test_synthetic_data.py
starfish/core/test/__init__.py
starfish/core/test/factories.py
starfish/core/test/test_display.py
starfish/core/test/test_multiprocessing_workflow.py
starfish/core/test/test_synthetic_spot_creation.py
starfish/core/types/__init__.py
starfish/core/types/_constants.py
starfish/core/types/_decoded_spots.py
starfish/core/types/_functionsource.py
starfish/core/types/_spot_attributes.py
starfish/core/types/_spot_finding_results.py
starfish/core/types/_validated_table.py
starfish/core/types/test/__init__.py
starfish/core/types/test/test_decoded_spots.py
starfish/core/util/__init__.py
starfish/core/util/argparse.py
starfish/core/util/clock.py
starfish/core/util/config.py
starfish/core/util/enum.py
starfish/core/util/exec.py
starfish/core/util/levels.py
starfish/core/util/logging.py
starfish/core/util/try_import.py
starfish/core/util/click/__init__.py
starfish/core/util/test/__init__.py
starfish/core/util/test/test_levels.py
starfish/core/util/test/test_preserve_float_range.py
starfish/experiment/__init__.py
starfish/experiment/builder.py
starfish/spacetx_format/examples/codebook/codebook.json
starfish/spacetx_format/examples/codebook/codebook_diagonal.json
starfish/spacetx_format/examples/codebook/codebook_diagonal_inferred_value.json
starfish/spacetx_format/examples/experiment/dartfish_experiment.json
starfish/spacetx_format/examples/experiment/experiment.json
starfish/spacetx_format/examples/experiment/no_fov_manifest.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_x_scalar.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_x_single.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_y_scalar.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_y_single.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_z_single.json
starfish/spacetx_format/examples/field_of_view/coordinates_bad_z_triple.json
starfish/spacetx_format/examples/field_of_view/coordinates_good_max.json
starfish/spacetx_format/examples/field_of_view/coordinates_good_min.json
starfish/spacetx_format/examples/field_of_view/dartfish_field_of_view.json
starfish/spacetx_format/examples/field_of_view/dartfish_nuclei.json
starfish/spacetx_format/examples/field_of_view/field_of_view.json
starfish/spacetx_format/examples/field_of_view/too_large.json
starfish/spacetx_format/examples/fov_manifest/fov_manifest.json
starfish/spacetx_format/schema/experiment_4.0.0.json
starfish/spacetx_format/schema/experiment_5.0.0.json
starfish/spacetx_format/schema/extras.json
starfish/spacetx_format/schema/fov_manifest_0.0.0.json
starfish/spacetx_format/schema/fov_manifest_0.1.0.json
starfish/spacetx_format/schema/version.json
starfish/spacetx_format/schema/codebook_0.0.0/codebook.json
starfish/spacetx_format/schema/codebook_0.0.0/codeword.json
starfish/spacetx_format/schema/field_of_view_0.0.0/field_of_view.json
starfish/spacetx_format/schema/field_of_view_0.0.0/tiles/coordinates.json
starfish/spacetx_format/schema/field_of_view_0.0.0/tiles/indices.json
starfish/spacetx_format/schema/field_of_view_0.0.0/tiles/tiles.json
starfish/spacetx_format/schema/field_of_view_0.1.0/field_of_view.json
starfish/spacetx_format/schema/field_of_view_0.1.0/tiles/coordinates.json
starfish/spacetx_format/schema/field_of_view_0.1.0/tiles/indices.json
starfish/spacetx_format/schema/field_of_view_0.1.0/tiles/tiles.json
starfish/test/__init__.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/util/__init__.py
starfish/util/plot.py