angelolab / ark-analysis

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• overwrite_option
• 0.3.0
• 0.3.1
• 857-refactor-mask-generation
• 883-unable-to-create-overlay-image-using-mesmer-output-tiff-and-input-tiff-images
• LDA_training_and_inference
• add-citation
• add-requests
• add_back_px_chan_norm
• add_nuc_count
• add_single_proc
• adjust_load_tiled_imgs
• adjust_pixel_overlays
• adjusting_PKG_FOLDER
• alt_dtype_handling
• ark-3.6
• ark-3.7-docker
• ark_pipeline
• arrow_patch
• auto-upload-patch
• batching-progress-bar
• binning_labels_part_2
• boxplot_func
• bug-583-verify-in-np-array
• bump_kiosk
• bump_version
• candace_fix
• cbar_minor_ticks
• cell_99
• cell_cluster
• cell_label_add
• cell_table_slow
• celltable_im_dtype_fix
• chan_stand
• channel_unsort
• check_cov
• ci/wheel_building
• cleanup_imports
• close-num-rand-asymmetry
• close-num-rand-speedup
• close_num_fix
• cluster_boost
• cluster_fix
• cluster_mask_speed
• cluster_viz
• colorbar_scale
• combined-notebook
• condence_cluster_data
• condense_label_save
• consensus_clear
• consensus_cluster
• consensus_fix
• context-dependent-randomization
• context-tests
• context_spatial
• contributing_guidelines
• contributing_update
• core_fix
• create_mantis_proj_dup
• cryptography_fix
• custom_smooth
• data_format
• data_models_readme
• data_prefix
• data_utils_clean
• deepcell-task
• deepcell_flex_size
• deepcell_json_decode
• deepcell_path_patch
• deepcell_service_logs
• default_heatmap
• default_zip
• delete_feather
• dependabot/pip/docs/ipython-7.16.3
• dependabot/pip/docs/ipython-8.10.0
• design_doc
• different_image_sizes
• dim_red_clean
• dist-lim-correction
• dist_mat_index
• doc_org
• doc_org_redux
• docker-command-fix
• docker-local-changes
• docker-test
• docker_badge
• docker_build_instructions
• docker_deploy
• docker_doc_deprecate
• docker_flowsom_install_fix
• docker_memory
• docker_open_scripts_dir
• docker_port
• docker_start_add
• docker_tag_sec
• docker_update
• docker_windows
• docker_windows_doc_fix_sri
• docs/cell_table_info
• download_mibi
• download_url_remove_v
• empty_seg_mask
• enrich_random_patch
• enrichment-distance-hack
• example_dataset
• example_dataset/caching
• example_dataset/cropped_fov0
• example_dataset/local_caching
• example_dataset/merged_dataset
• example_dataset/nb2
• example_dataset/nb3
• example_dataset/nb4
• example_dataset/overwrite_existing_docs
• example_dataset/spatial_analysis
• external_drive_docker_docs
• extraction-options
• extraction_bug
• faq
• feature/release_drafter
• feature_0_1
• fiber-segmentation
• file-delimiter-fix
• fix-close-cell-random
• fix-setup-typo
• fix_double_testing
• fix_np_float
• fix_pixie_notebook_description
• flex_som_map
• flowsom_notes
• fov_masks_separate_dir
• fov_name_parsing_fix
• generic-batching-decorators
• gh-readonly-queue/main/pr-1006-d547efb338cda0f2948052efd6045392632fd9ac
• gh-readonly-queue/main/pr-1007-d7bbe1501d4e8828ca797e7ef7cf7afa2832811b
• gh-readonly-queue/main/pr-1011-5acbee26a2b698fc47d2a0c3428f35ad115e4200
• gh-readonly-queue/main/pr-1012-67a1a589c35485d7a534f87c1b48393a3681fff7
• gh-readonly-queue/main/pr-1025-e604956d7c9e86a018a45df13d78d8eff0d33c17
• gh-readonly-queue/main/pr-1027-7823f9d92dc3d22aebb861c93b7d40404af3e077
• gh-readonly-queue/main/pr-1031-94e63630fc0349bde4b40fb0a413c70c04825881
• gh-readonly-queue/main/pr-1033-82b93128fc98fbe2d9a3d867ea2dfeb7c552fc44
• gh-readonly-queue/main/pr-1047-2ba38f28910fb3570ae866cd95518deb1f1733f5
• gh-readonly-queue/main/pr-1048-511524c33084dfaab93b2a45036b256d2e688f3a
• gh-readonly-queue/main/pr-1050-b4baca2f277491cd6e395a5602d1cbcd67fe326a
• gh-readonly-queue/main/pr-1051-963763fd11afcd58f76bc187126c212fd3d52025
• gh-readonly-queue/main/pr-1053-59b43c86e857582a225ac831fd59c7f92ae9bb35
• gh-readonly-queue/main/pr-1057-e5d0fd97156f7a096025898abf3bcd5c5c71296b
• gh-readonly-queue/main/pr-1058-c575ead1ad98f072b84d4a116822b107d951eee8
• gh-readonly-queue/main/pr-1060-d8e9577c87bdb5509e5e0b1c7b6d580c412d088d
• gh-readonly-queue/main/pr-1061-58128c1da2b7756feb5c189355aa79cd6395fcbd
• gh-readonly-queue/main/pr-1067-e4caefeb5e1c8f74939efe18b1dd3d8382aec5db
• gh-readonly-queue/main/pr-1069-ad859b234b7feda60acf3fd3ebb72e80756750cd
• gh-readonly-queue/main/pr-1083-11de0b045597d238e5a2f9d8ae559adf38733f66
• gh-readonly-queue/main/pr-1092-51dd1c42c7c215cdcd6140765ec42ec08ec5370d
• gh-readonly-queue/main/pr-1093-99a9abbdac94f2394eb71159d4f13515ac614f72
• gh-readonly-queue/main/pr-1101-d3e9e4a3f946eee5d6482c97c78eef58337f5d18
• gh-readonly-queue/main/pr-1104-871d535704c90b50b20680770048cbc80dc5b64a
• gh-readonly-queue/main/pr-1107-3ab7f9dff92fc7411c0808eeba4cc49d0d626416
• gh-readonly-queue/main/pr-1110-63ee8ffad1fd65c1d435cc8aa4a6fb10e67c3bd0
• gh-readonly-queue/main/pr-1114-f3391e56b8790d9a70602680dad6d396e80d75e7
• gh-readonly-queue/main/pr-1123-8877213489a5c35e825cbcaa2a5140ebfdbe6f6f
• gh-readonly-queue/main/pr-1124-10aa4a14f1c7d24c2a840976098683019f1df33b
• gh-readonly-queue/main/pr-1126-dac262e4359a36476fb5e6b74f65e1538ad58284
• gh-readonly-queue/main/pr-1127-9bd4a39cc0532777b269ad41257ffe4def94eeeb
• gh-readonly-queue/main/pr-1130-a3c08d67a17b40d9a71fdacf597853d1a3e359c7
• gh-readonly-queue/main/pr-1134-da4013ca00f0da11e18b77a8506696fc4f05329b
• gh-readonly-queue/main/pr-1139-c87731413a5584fef127b73b8468e6cd46a2e662
• gh-readonly-queue/main/pr-1144-aad0872f18ce63011fe47bf9c8e84b5e66636883
• gh-readonly-queue/main/pr-1158-cb8ccdb9c18ab8b8287149f0ab13eeb3366d3593
• gh-readonly-queue/main/pr-1159-301e344f0ffbedafaad282c52c801e7713272f85
• gh-readonly-queue/main/pr-894-a4b2841ce9600938f2f8e6aee04e925008c10858
• gh-readonly-queue/main/pr-908-1f3859f53982d9c1dece38f92af570d99b8b4466
• gh-readonly-queue/main/pr-935-39089035bea2d2167380f0b22881d8f9b4a3f515
• gh-readonly-queue/main/pr-939-8d28c2cdcc76eded9a9da4a81b1e5ee2b5424ece
• gh-readonly-queue/main/pr-942-7b37816d667c39e4fbad124a22fe273a69728520
• gh-readonly-queue/main/pr-946-f6e0d2a56b0231502fc61cf0a65ce2d7a2d6b644
• gh-readonly-queue/main/pr-951-ad4e42fd7bf84a971b9719618b073d887746f6c8
• gh-readonly-queue/main/pr-953-8293e1fbf57ea22cb59a09fa46d61a461f57d5ed
• gh-readonly-queue/main/pr-955-f9a412b454ec0e25e336cd99607312b89776ece9
• gh-readonly-queue/main/pr-958-bfc53b7d6f7bdf96ef95dd03ea84f9dfefc74dc9
• gh-readonly-queue/main/pr-959-8e5366783c2ae5b26ff9cad32f2a198f841815f5
• gh-readonly-queue/main/pr-960-68a3d954090f6ec36d066bca4928e32772b390db
• gh-readonly-queue/main/pr-966-ac64b0e8b6e3df54de30e5a9fc20f5d132b51fed
• gh-readonly-queue/main/pr-973-79177931bdfaa98cae63b0a33c6aee289f93fc9a
• gh-readonly-queue/main/pr-978-675a7e1f2ee3c8faa16a69800ee2271d355474a0
• gh-readonly-queue/main/pr-981-dc9854979077335b04af85a0030f301bb2d7365b
• gh-readonly-queue/main/pr-983-061a128886947bf3b0c22f30623fb6e0fe5e647e
• gh-readonly-queue/main/pr-991-2af302d202e64c63d0a19bc0fba40527302adca5
• gh-readonly-queue/main/pr-993-c0c31edac976dbb6ecda5d101de1cbd3a880cc78
• gh-readonly-queue/main/pr-994-aa4f11452cf1b2dbdb93fb0d1378aabc892cedd3
• gh-readonly-queue/main/pr-998-cb8084748a94e9004e9685075cdf8e7d783814d3
• gh-readonly-queue/main/pr-999-e663b04156d6b5e299d33a48dfc3314df6601d5d
• git_install_instructions
• github-actions-from-template
• global-settings
• google-drive-documentation
• google-drive-hotfix
• google-drive-integration
• ignore_hidden_files
• improve_jupyter_launch
• initial_deploy
• input_validation
• integrated_plotting
• integrated_plotting_function
• integrated_plotting_functions
• ipympl_fix
• iter_viz
• iterable_dtypes_fix
• jitter_signal
• jupyter_lab
• k_means
• k_means_mat
• kmeans_neighborhood_nb_update
• kmeans_nh_no_excluded_channels_fix
• kmeans_seed
• landing_doc
• lda_metrics
• line-length-fix
• line_length
• load_tree_wrong_chan_name
• load_utils/load_tif
• load_utils_fix
• load_utils_float_conversion_warning
• local-updating
• localize-mibitiff
• low_contrast_warning
• m1_ark_setup
• main
• mantis/generalize_seg_mask_suffix
• mantis/img_suffix
• mantis_assign_cells
• mantis_dir
• mantis_seg_suffix
• marker_verify
• mask_index_fix
• master
• meta_dup
• meta_zscore_slider
• metacluster_gui
• metacluster_width
• mibilib-workaround
• mibitiff-throw-error
• mibitiff_cell_mat
• mixing_score
• modify_nuc_labels
• morph_add
• morph_doc
• morph_index_fix
• move_meta_rename
• multiarch_docker
• nbsphinx_delete
• neigh_index
• neighbor_notebook
• neighborhood_progress
• new_cluster_boost
• new_rand_mod
• new_som
• next_release_v0.4.1
• next_release_v0.4.2
• next_release_v0.4.3
• next_release_v0.4.4
• next_release_v0.5.0
• next_release_v0.5.1
• ngreenwald-patch-1
• ngreenwald-patch-1-1
• no-contrast-check
• normal_transform
• notebook_reorg
• notebook_tests
• notebook_update_test_bash_cmd
• nuc_filter
• nuc_memb_viz
• nuclear_counts_false
• nuclear_fix
• nuclei_split_threshold
• ome_tiff
• optimization/compressed_csvs
• optimize_df_merging
• overlay_cmap
• parallel_som
• patch_contributing
• patch_kmeans_min
• patch_mask_gen
• patch_tests
• patch_virtualenv
• pin-docutils
• pix_preprocessing
• pixel_channel_mem
• pixel_mask
• pixel_mask_batches
• pixel_mask_boost
• pixel_mask_index
• pixel_overlay_patch
• pixel_path_fix
• pixel_som_verify_fix
• pixie/filter_with_nuclear_mask
• pixie_authorship
• pixie_clean
• plot_clustering_result
• plot_overlay_fix
• plot_utils_clean
• point_remove
• post_clustering
• preprocess_pixie_cell
• processing_branch
• prog-bar-fix
• progress_bars
• propagate_fovs
• py_consensus
• pyflowsom_add
• pypi_bugfix
• pypi_debug
• pypi_name
• pypi_req_fix
• pypi_setup
• python-3.6
• python-3.7
• python-3.8+AppleSilicon_support
• python_3.7
• python_3.7_version_download_fix
• qc_metric_moly
• qc_metrics
• r_som
• rand_mod
• readd_docker_update
• readme-clarification
• readme/pipeline_flowchart/pixie
• readme_badges
• readme_build_fix
• readme_discussion
• rebuild_docker
• refactor_dist_mat
• regionprops_extension
• regionprops_sanitization
• remap
• remove_MIBItiff
• remove_deterministic
• remove_file_extension_fix
• remove_googledrivepath_dead_code
• remove_manual_clustering_nb
• remove_mibi_dir
• remove_mibitiff_in_notebooks
• remove_rplots
• remove_templates
• req_ranges
• requirements_test
• rescale_deepcell_input
• rescale_doc
• restart_som
• retrain_pixel_som
• rosetta_matrix
• rtd_path
• rtd_reorg
• scale_arg_debug
• seg_clean
• seg_dir_cluster
• seg_opt
• seperate_folders
• settings_name_update
• setup_reqs
• som
• som_batch
• som_cluster
• som_cluster_test
• som_compress
• som_dtype_pass
• som_heatmap
• som_memory
• som_norm
• som_norm_path_fix
• som_pre
• som_pre_test
• som_updates
• spatial-analysis-fov-batching
• spatial-analysis-nb-update
• spatial-memory-cleanup
• spatial_LDA
• spatial_LDA_viz
• spatial_enrichment_loading
• spatial_enrichment_test
• spatial_utils_clean
• speed_tests
• sphinx_setup
• sphinx_style
• split_nuclei_bugfix
• split_som_modules
• start-docker-upgrade
• start_cell_cluster
• start_docker_script_fix
• stitch_test
• subcellular_loc_notebook
• subset_channel_avg
• subset_som
• substr-matching
• substr_fix
• syn_data_clean
• template_developer_flag
• templates_rename
• test-utils
• test_book
• test_ignore
• test_utils
• tiff_ext
• tiff_standard
• tile_viz
• tiled_images
• tiling_add
• tma
• tmi/utils
• travis_ci_docker_tags
• travis_fix
• travis_mult
• unbatch_cell_table
• unbatch_mask_gen
• unbatch_spatial
• update-flag
• update_blur_description
• update_contributing_doc
• update_docker_script
• update_seg_save
• v0.2.10
• v0.2.11
• v0.2.4
• v0.2.5
• v0.2.6
• v0.2.7
• v0.2.8
• v0.2.9
• v0.3.0
• v0.3.1
• v0.3.2
• v0.4.0
• v0.4.1
• v0.4.2
• v0.4.3
• v0.4.4
• v0.5.0
• v0.5.1
• validate_path_update
• validate_paths_usage
• verify_err_msg
• verify_norm_chans
• verify_refactor
• verify_warnings
• virt_env_doc
• virt_env_doc_redux
• visualization_example
• viz_patch
• windows_docker_restart
• workshop_vods
• wsl_doc
• xarray_exp
• z_slider_fix
• zero_col_cell
• zip_compression

Add a hidden parameter to overwrite certain portions of the pipeline (#914)