angelolab / ark-analysis

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LAST BUILD ON BRANCH gh-readonly-queue/main/pr-1092-51dd1c42c7c215cdcd6140765ec42ec08ec5370d

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• gh-readonly-queue/main/pr-1092-51dd1c42c7c215cdcd6140765ec42ec08ec5370d
• 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
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• cell_label_add
• cell_table_slow
• celltable_im_dtype_fix
• chan_stand
• channel_unsort
• check_cov
• ci/wheel_building
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• 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
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• dist_mat_index
• doc_org
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• docker-command-fix
• docker-local-changes
• docker-test
• docker_badge
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• docker_windows_doc_fix_sri
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• enrich_random_patch
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• example_dataset
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• example_dataset/nb2
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• example_dataset/nb4
• example_dataset/overwrite_existing_docs
• example_dataset/spatial_analysis
• external_drive_docker_docs
• extraction-options
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• feature_0_1
• fiber-segmentation
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• fix_np_float
• flex_som_map
• flowsom_notes
• fov_masks_separate_dir
• fov_name_parsing_fix
• generic-batching-decorators
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• gh-readonly-queue/main/pr-1159-301e344f0ffbedafaad282c52c801e7713272f85
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• 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
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• gh-readonly-queue/main/pr-960-68a3d954090f6ec36d066bca4928e32772b390db
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• 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
• overwrite_option
• 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
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• remove_rplots
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• req_ranges
• requirements_test
• rescale_deepcell_input
• rescale_doc
• restart_som
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• rtd_reorg
• scale_arg_debug
• seg_clean
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• seperate_folders
• settings_name_update
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• som
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• som_dtype_pass
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• 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
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• start_docker_script_fix
• stitch_test
• subcellular_loc_notebook
• subset_channel_avg
• subset_som
• substr-matching
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• template_developer_flag
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• tiff_ext
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• tiling_add
• tma
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• travis_ci_docker_tags
• travis_fix
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• 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
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• v0.2.5
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• v0.4.0
• v0.4.1
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• v0.5.0
• v0.5.1
• validate_path_update
• validate_paths_usage
• verify_err_msg
• verify_norm_chans
• verify_refactor
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• virt_env_doc
• virt_env_doc_redux
• visualization_example
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• windows_docker_restart
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• wsl_doc
• xarray_exp
• z_slider_fix
• zero_col_cell
• zip_compression

Build # 8839412992

Build Type

push

github

Committed by web-flow

Commit Message

Generalized masking (#1092)

* init

* tests

* notebook

* use ez_seg.composite.composite_builder

* fix composite_dir if statement

* use _create_object_mask instead of create_mask

* remove squidpy requirement

* remove dask dependecy

* pycodestyle

* notebook updates

* notebook tweaks

* feedback tweaks

* feedback tweaks II

* pin torchdata

* pin pytorch

* remove pytorch pin

* Test with torch==2.2.0, this worked with Kausi

* Handle case where composite_directory needs explicit conversion to pathlib.Path if of type str

---------

Co-authored-by: alex-l-kong <alkong@ucdavis.edu>

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