├── .dockerignore ├── .flake8 ├── .gitattributes ├── .github ├── .python-version ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ ├── feature_request.md │ └── user-story.md ├── copilot-instructions.md ├── copilot-setup-steps.yml ├── dependabot.yml └── workflows │ ├── codeql.yml │ └── starfish-prod-ci.yml ├── .gitignore ├── .hgtags ├── CHANGELOG.md ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── REQUIREMENTS.txt ├── codecov.yml ├── docker └── Dockerfile ├── docs ├── Makefile └── source │ ├── _static │ ├── README │ ├── design │ │ ├── decoding_flowchart.png │ │ ├── field_of_view.png │ │ ├── imagestack.png │ │ ├── ivana-cajina-asuyh-_ZX54-unsplash.jpg │ │ ├── ivana-cajina-asuyh-_ZX54-unsplash.png │ │ ├── linear_codebook_1.png │ │ ├── linear_codebook_2.png │ │ ├── logo-solo.png │ │ ├── logo-transparent.png │ │ ├── logo.pdf │ │ ├── logo.png │ │ ├── multiplex_codebook_1.png │ │ ├── multiplex_codebook_2.png │ │ ├── napari-viewer.png │ │ ├── onehot_codebook_1.png │ │ ├── onehot_codebook_2.png │ │ ├── pipeline-diagram.pdf │ │ ├── pipeline-diagram.png │ │ ├── processing_model.png │ │ └── tracebuilder_decisiontree.png │ ├── example_data_files │ │ ├── README.rst │ │ ├── decoded.csv │ │ └── decoded.nc │ ├── favicon.ico │ ├── images │ │ ├── aws-tutorial-figure1.png │ │ ├── aws-tutorial-figure2.png │ │ ├── aws-tutorial-figure3.png │ │ ├── aws-tutorial-figure4.png │ │ ├── aws-tutorial-figure5.png │ │ ├── aws-tutorial-figure6.png │ │ ├── aws-tutorial-figure7.png │ │ ├── quickstart-napari-screenshot-2.png │ │ ├── quickstart-napari-screenshot-3.png │ │ ├── quickstart-napari-screenshot-4.png │ │ ├── quickstart-napari-screenshot-5.png │ │ └── quickstart-napari-screenshot.png │ ├── my-styles.css │ └── starfish-aws-templates.zip │ ├── _templates │ ├── layout.html │ └── relations.html │ ├── about │ └── index.rst │ ├── api │ ├── data_structures │ │ ├── binary_mask.rst │ │ ├── codebook.rst │ │ ├── decoded_intensity_table.rst │ │ ├── experiment.rst │ │ ├── expression_matrix.rst │ │ ├── field_of_view.rst │ │ ├── image_stack.rst │ │ ├── index.rst │ │ ├── intensity_table.rst │ │ └── label_image.rst │ ├── datasets │ │ └── index.rst │ ├── display │ │ └── index.rst │ ├── experiment_builder │ │ └── index.rst │ ├── image │ │ └── index.rst │ ├── index.rst │ ├── morphology │ │ └── index.rst │ ├── plot_utils │ │ └── index.rst │ ├── slicedimage │ │ └── index.rst │ ├── spots │ │ └── index.rst │ ├── types │ │ └── index.rst │ ├── utils │ │ ├── config.rst │ │ ├── index.rst │ │ └── logging.rst │ └── validation │ │ └── index.rst │ ├── conf.py │ ├── developer_guide │ └── index.rst │ ├── help_and_reference │ ├── available_datasets │ │ └── index.rst │ ├── configuration │ │ └── index.rst │ ├── data_model │ │ └── index.rst │ ├── glossary │ │ └── glossary.rst │ ├── index.rst │ ├── request_support │ │ └── index.rst │ ├── spacetx-format │ │ ├── SpaceTxFormat │ │ │ └── index.rst │ │ ├── Validation │ │ │ └── index.rst │ │ └── index.rst │ └── spacetx_consortium │ │ └── index.rst │ ├── index.rst │ ├── installation │ └── index.rst │ └── user_guide │ ├── index.rst │ ├── processing_at_scale │ └── index.rst │ └── working_with_starfish_outputs │ ├── DecodedSpots │ └── index.rst │ ├── ExpressionMatrix │ └── index.rst │ ├── IntensityTable │ └── index.rst │ ├── SegmentationMask │ └── index.rst │ └── index.rst ├── examples ├── README.txt ├── data_formatting │ ├── README.txt │ ├── plot_format_structured_data.py │ └── plot_format_tilefetcher.py ├── data_formatting_examples │ ├── README.txt │ ├── format_baristaseq.py │ ├── format_imc_data.py │ ├── format_iss_breast_data.py │ ├── format_iss_data.py │ ├── format_merfish_U2OS_data.py │ ├── format_osmfish.py │ ├── format_seqFISH.py │ └── format_starmap.py ├── data_loading │ ├── README.txt │ ├── plot_loading_data.py │ └── plot_tilefetcher_loader.py ├── how_to │ ├── README.txt │ ├── assess_spotfindingresults.py │ ├── blob_detector.py │ ├── clip.py │ ├── clip_percentile_to_zero.py │ ├── clip_value_to_zero.py │ ├── imshow_plane.py │ ├── intensity_histogram.py │ ├── local_max_peak_finder.py │ ├── match_histograms.py │ ├── metric_distance.py │ ├── per_round_max_channel.py │ ├── plot_display.py │ ├── simple_lookup_decoder.py │ ├── tracebuildingstrategies.py │ └── trackpy_local_max_peak_finder.py ├── pipelines │ ├── 3d_smFISH.py │ ├── README.txt │ ├── baristaseq_pipeline.py │ ├── dartfish_pipeline.py │ ├── data │ ├── iss_pipeline.py │ ├── merfish_pipeline.py │ ├── osmfish_pipeline.py │ ├── starmap_pipeline.py │ ├── starmap_pipeline.py.skip │ └── subdir.mk ├── quick_start │ ├── README.txt │ └── plot_quick_start.py └── tutorials │ ├── README.txt │ ├── RoiSet.zip │ ├── assigning_spots.py │ ├── dapi_Probabilities.h5 │ ├── ilastik_segmentation.py │ ├── manual_segmentation.py │ ├── merfish_dapi.ilp │ ├── normalize_intensity_distributions.py │ ├── normalize_intensity_values.py │ ├── pixelbased_decoding.py │ ├── plot_illumination_correction.py │ ├── plot_image_manipulations.py │ ├── plot_image_registration.py │ ├── plot_tissue_specific_corrections.py │ ├── run_ilastik.sh │ ├── spotbased_decoding.py │ ├── transforms_list.json │ └── watershed_segmentation.py ├── notebooks ├── BaristaSeq.ipynb ├── DARTFISH.ipynb ├── ISS.ipynb ├── MERFISH.ipynb ├── STARmap.ipynb ├── SeqFISH.ipynb ├── Starfish_simulation.ipynb ├── data │ └── EXP-17-BP3597_hyb1_Aldoc_pos_33.pkl ├── osmFISH.ipynb ├── py │ ├── BaristaSeq.py │ ├── DARTFISH.py │ ├── ISS.py │ ├── MERFISH.py │ ├── README.txt │ ├── STARmap.py │ ├── STARmap.py.skip │ ├── SeqFISH.py │ ├── SeqFISH.py.skip │ ├── Starfish_simulation.py │ ├── Starfish_simulation.py.skip │ ├── data │ ├── osmFISH.py │ └── smFISH.py ├── smFISH.ipynb └── subdir.mk ├── paper ├── paper.bib └── paper.md ├── pyproject.toml ├── pytest.ini ├── readthedocs.yml ├── requirements ├── REQUIREMENTS-CI.txt ├── REQUIREMENTS-CI.txt.in ├── REQUIREMENTS-JUPYTER.txt ├── REQUIREMENTS-JUPYTER.txt.in ├── REQUIREMENTS-NAPARI-CI.txt └── REQUIREMENTS-NAPARI-CI.txt.in ├── setup.py ├── starfish ├── REQUIREMENTS-STRICT.txt ├── __init__.py ├── __main__.py ├── config.py ├── core │ ├── __init__.py │ ├── _display.py │ ├── _version.py │ ├── codebook │ │ ├── __init__.py │ │ ├── _format.py │ │ ├── codebook.py │ │ └── test │ │ │ ├── __init__.py │ │ │ ├── factories.py │ │ │ ├── test_approximate_nearest_code.py │ │ │ ├── test_code_length.py │ │ │ ├── test_from_code_array.py │ │ │ ├── test_metric_decode.py │ │ │ ├── test_normalize_code_traces.py │ │ │ ├── test_per_round_max_decode.py │ │ │ ├── test_synthetic_one_hot_codebook.py │ │ │ └── test_to_json.py │ ├── config │ │ ├── __init__.py │ │ └── test │ │ │ ├── __init__.py │ │ │ └── test_config.py │ ├── errors.py │ ├── experiment │ │ ├── __init__.py │ │ ├── builder │ │ │ ├── __init__.py │ │ │ ├── builder.py │ │ │ ├── defaultproviders.py │ │ │ ├── inplace.py │ │ │ ├── orderediterator.py │ │ │ ├── providers.py │ │ │ ├── structured_formatter.py │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ ├── factories │ │ │ │ ├── __init__.py │ │ │ │ ├── all_purpose.py │ │ │ │ └── unique_tiles.py │ │ │ │ ├── structured_formatter │ │ │ │ ├── __init__.py │ │ │ │ ├── test_multiple_fov.py │ │ │ │ ├── test_single_fov.py │ │ │ │ ├── test_tilepath.py │ │ │ │ └── util.py │ │ │ │ ├── test_inplace.py │ │ │ │ ├── test_orderediterator.py │ │ │ │ └── test_small_axis.py │ │ ├── experiment.py │ │ ├── test │ │ │ ├── __init__.py │ │ │ ├── test_experiment.py │ │ │ ├── test_get_image_repr_warning.py │ │ │ └── test_version.py │ │ └── version.py │ ├── expression_matrix │ │ ├── __init__.py │ │ ├── concatenate.py │ │ ├── expression_matrix.py │ │ └── test │ │ │ ├── __init__.py │ │ │ ├── test_concatenate.py │ │ │ └── test_serialization.py │ ├── image │ │ ├── Filter │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── bandpass.py │ │ │ ├── call_bases.py │ │ │ ├── clip.py │ │ │ ├── clip_percentile_to_zero.py │ │ │ ├── clip_value_to_zero.py │ │ │ ├── element_wise_mult.py │ │ │ ├── gaussian_high_pass.py │ │ │ ├── gaussian_low_pass.py │ │ │ ├── ilastik_pre_trained_probability.py │ │ │ ├── laplace.py │ │ │ ├── linear_unmixing.py │ │ │ ├── map.py │ │ │ ├── match_histograms.py │ │ │ ├── mean_high_pass.py │ │ │ ├── reduce.py │ │ │ ├── richardson_lucy_deconvolution.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ ├── test_api_contract.py │ │ │ │ ├── test_call_bases.py │ │ │ │ ├── test_filter.py │ │ │ │ ├── test_histogram_matching.py │ │ │ │ ├── test_linear_unmixing.py │ │ │ │ ├── test_map.py │ │ │ │ ├── test_reduce.py │ │ │ │ ├── test_white_tophat.py │ │ │ │ └── test_zero_by_channel_magnitude.py │ │ │ ├── util.py │ │ │ ├── white_tophat.py │ │ │ └── zero_by_channel_magnitude.py │ │ ├── Segment │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ └── watershed.py │ │ ├── __init__.py │ │ └── _registration │ │ │ ├── ApplyTransform │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ └── test_warp.py │ │ │ └── warp.py │ │ │ ├── LearnTransform │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ └── test_translation.py │ │ │ └── translation.py │ │ │ ├── __init__.py │ │ │ ├── _format.py │ │ │ ├── test │ │ │ ├── __init__.py │ │ │ └── test_transforms_list.py │ │ │ └── transforms_list.py │ ├── imagestack │ │ ├── __init__.py │ │ ├── dataorder.py │ │ ├── imagestack.py │ │ ├── indexing_utils.py │ │ ├── parser │ │ │ ├── __init__.py │ │ │ ├── _key.py │ │ │ ├── _tiledata.py │ │ │ ├── crop.py │ │ │ ├── numpy │ │ │ │ └── __init__.py │ │ │ ├── tilefetcher │ │ │ │ ├── __init__.py │ │ │ │ └── _parser.py │ │ │ ├── tileset │ │ │ │ ├── __init__.py │ │ │ │ └── _parser.py │ │ │ └── xarray │ │ │ │ └── __init__.py │ │ ├── physical_coordinates.py │ │ └── test │ │ │ ├── __init__.py │ │ │ ├── factories │ │ │ ├── __init__.py │ │ │ ├── all_purpose.py │ │ │ ├── from_codebook.py │ │ │ ├── synthetic_stack.py │ │ │ ├── unique_tiles.py │ │ │ └── with_coords.py │ │ │ ├── imagestack_test_utils.py │ │ │ ├── test_apply.py │ │ │ ├── test_coordinates.py │ │ │ ├── test_cropped_load.py │ │ │ ├── test_export.py │ │ │ ├── test_from_numpy_array.py │ │ │ ├── test_from_tilefetcher.py │ │ │ ├── test_from_xarray.py │ │ │ ├── test_index.py │ │ │ ├── test_labeled_indices.py │ │ │ ├── test_max_proj.py │ │ │ ├── test_metadata.py │ │ │ ├── test_physical_coordinate_calculator.py │ │ │ ├── test_slice_ops.py │ │ │ └── test_slicedimage_dtype.py │ ├── intensity_table │ │ ├── __init__.py │ │ ├── concatenate.py │ │ ├── decoded_intensity_table.py │ │ ├── intensity_table.py │ │ ├── intensity_table_coordinates.py │ │ ├── overlap.py │ │ └── test │ │ │ ├── __init__.py │ │ │ ├── factories.py │ │ │ ├── test_concatenate.py │ │ │ ├── test_empty_intensity_table.py │ │ │ ├── test_from_imagestack.py │ │ │ ├── test_from_spot_data.py │ │ │ ├── test_intensity_table_coords.py │ │ │ ├── test_intensity_table_serialization.py │ │ │ ├── test_overlap.py │ │ │ ├── test_stack_intensity_table_reshaping.py │ │ │ ├── test_synthetic_intensities.py │ │ │ └── test_to_mermaid.py │ ├── morphology │ │ ├── Binarize │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ └── test_threshold.py │ │ │ └── threshold.py │ │ ├── Filter │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── areafilter.py │ │ │ ├── map.py │ │ │ ├── min_distance_label.py │ │ │ ├── reduce.py │ │ │ ├── structural_label.py │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ ├── test_areafilter.py │ │ │ │ ├── test_map.py │ │ │ │ └── test_reduce.py │ │ ├── Merge │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── simple.py │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ └── test_simple.py │ │ ├── Segment │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ └── watershed.py │ │ ├── __init__.py │ │ ├── binary_mask │ │ │ ├── __init__.py │ │ │ ├── _io.py │ │ │ ├── binary_mask.py │ │ │ ├── expand.py │ │ │ └── test │ │ │ │ ├── RoiSet.zip │ │ │ │ ├── __init__.py │ │ │ │ ├── factories.py │ │ │ │ ├── test_binary_mask.py │ │ │ │ ├── test_expand.py │ │ │ │ ├── test_from_binary_arrays_and_ticks.py │ │ │ │ └── test_from_label_array_and_ticks.py │ │ ├── label_image │ │ │ ├── __init__.py │ │ │ ├── label_image.py │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ └── test_label_image.py │ │ └── util.py │ ├── pipeline │ │ ├── __init__.py │ │ └── algorithmbase.py │ ├── segmentation_mask │ │ ├── __init__.py │ │ └── segmentation_mask.py │ ├── spacetx_format │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── test │ │ │ └── test_validate.py │ │ ├── test_codebook.py │ │ ├── test_coordinates.py │ │ ├── test_experiment.py │ │ ├── test_field_of_view.py │ │ ├── test_fov_manifest.py │ │ ├── test_fuzz.py │ │ ├── util.py │ │ └── validate_sptx.py │ ├── spots │ │ ├── AssignTargets │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ └── label.py │ │ ├── DecodeSpots │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── check_all_decoder.py │ │ │ ├── check_all_funcs.py │ │ │ ├── metric_decoder.py │ │ │ ├── per_round_max_channel_decoder.py │ │ │ ├── simple_lookup_decoder.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ ├── test_check_all.py │ │ │ │ ├── test_composite_codebook.py │ │ │ │ ├── test_decoding_without_spots.py │ │ │ │ ├── test_metric_decoder.py │ │ │ │ ├── test_nearest_neighbor_trace_builder.py │ │ │ │ ├── test_spot_finders.py │ │ │ │ └── test_trace_builders.py │ │ │ ├── trace_builders.py │ │ │ └── util.py │ │ ├── DetectPixels │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── combine_adjacent_features.py │ │ │ ├── pixel_spot_decoder.py │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ ├── test_calculate_mean_pixel_traces.py │ │ │ │ ├── test_create_spot_attributes.py │ │ │ │ ├── test_intensities_to_decoded_image.py │ │ │ │ └── test_targets_map.py │ │ ├── FindSpots │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── blob.py │ │ │ ├── local_max_peak_finder.py │ │ │ ├── spot_finding_utils.py │ │ │ ├── test │ │ │ │ ├── __init__.py │ │ │ │ ├── test_local_max_peak_finder.py │ │ │ │ ├── test_spot_detection.py │ │ │ │ └── test_synthetic_data.py │ │ │ └── trackpy_local_max_peak_finder.py │ │ └── __init__.py │ ├── starfish.py │ ├── test │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── test_display.py │ │ ├── test_multiprocessing_workflow.py │ │ └── test_synthetic_spot_creation.py │ ├── types │ │ ├── __init__.py │ │ ├── _constants.py │ │ ├── _decoded_spots.py │ │ ├── _functionsource.py │ │ ├── _spot_attributes.py │ │ ├── _spot_finding_results.py │ │ ├── _validated_table.py │ │ └── test │ │ │ ├── __init__.py │ │ │ ├── test_decoded_spots.py │ │ │ └── test_saving_spots.py │ └── util │ │ ├── __init__.py │ │ ├── argparse.py │ │ ├── click │ │ └── __init__.py │ │ ├── clock.py │ │ ├── config.py │ │ ├── enum.py │ │ ├── exec.py │ │ ├── levels.py │ │ ├── logging.py │ │ ├── test │ │ ├── __init__.py │ │ ├── test_levels.py │ │ └── test_preserve_float_range.py │ │ └── try_import.py ├── data.py ├── experiment │ ├── __init__.py │ └── builder.py ├── image.py ├── morphology.py ├── spacetx_format │ ├── README.md │ ├── examples │ │ ├── codebook │ │ │ ├── codebook.json │ │ │ ├── codebook_diagonal.json │ │ │ └── codebook_diagonal_inferred_value.json │ │ ├── experiment │ │ │ ├── dartfish_experiment.json │ │ │ ├── experiment.json │ │ │ └── no_fov_manifest.json │ │ ├── field_of_view │ │ │ ├── coordinates_bad_x_scalar.json │ │ │ ├── coordinates_bad_x_single.json │ │ │ ├── coordinates_bad_y_scalar.json │ │ │ ├── coordinates_bad_y_single.json │ │ │ ├── coordinates_bad_z_single.json │ │ │ ├── coordinates_bad_z_triple.json │ │ │ ├── coordinates_good_max.json │ │ │ ├── coordinates_good_min.json │ │ │ ├── dartfish_field_of_view.json │ │ │ ├── dartfish_nuclei.json │ │ │ ├── field_of_view.json │ │ │ └── too_large.json │ │ └── fov_manifest │ │ │ └── fov_manifest.json │ └── schema │ │ ├── README.md │ │ ├── codebook_0.0.0 │ │ ├── codebook.json │ │ └── codeword.json │ │ ├── experiment_4.0.0.json │ │ ├── experiment_5.0.0.json │ │ ├── extras.json │ │ ├── field_of_view_0.0.0 │ │ ├── field_of_view.json │ │ └── tiles │ │ │ ├── coordinates.json │ │ │ ├── indices.json │ │ │ └── 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