Index

A

AdaptiveFilterBarcodes (class in merlin.analysis.filterbarcodes) analysis_done_filename() (merlin.core.dataset.DataSet method) analysis_exists() (merlin.core.dataset.DataSet method)

analysis_tiff_description() (merlin.core.dataset.DataSet static method) AnalysisAlreadyExistsException AnalysisAlreadyStartedException AnalysisTask (class in merlin.core.analysistask)

B

BarcodeDB (class in merlin.util.barcodedb) BarcodeSavingParallelAnalysisTask (class in merlin.analysis.decode)

bit_list_to_int() (in module merlin.util.binary) build_parser() (in module merlin.merlin) (in module merlin.view.merlinview)

C

calculate_barcode_count_for_threshold() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) calculate_misidentification_rate_for_threshold() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) calculate_threshold_for_misidentification_rate() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) check_analysis_done() (merlin.core.dataset.DataSet method)

check_analysis_error() (merlin.core.dataset.DataSet method) check_analysis_started() (merlin.core.dataset.DataSet method) close_logger() (merlin.core.dataset.DataSet method) configure_environment() (in module merlin.merlin) CorrelationGlobalAlignment (class in merlin.analysis.globalalign)

D

DataFormatException DataSet (class in merlin.core.dataset) Decode (class in merlin.analysis.decode) decode_pixels() (merlin.util.decoding.PixelBasedDecoder method)

DeconvolutionPreprocess (class in merlin.analysis.preprocess) delete_analysis() (merlin.core.dataset.DataSet method) delete_hdf5_file() (merlin.core.dataset.DataSet method) delete_pandas_hdfstore() (merlin.core.dataset.DataSet method) delete_table() (merlin.core.dataset.DataSet method)

E

empty_database() (merlin.util.barcodedb.BarcodeDB method) (merlin.util.barcodedb.PyTablesBarcodeDB method) Executor (class in merlin.core.executor)

ExportBarcodes (class in merlin.analysis.exportbarcodes) extract_barcodes_with_index() (merlin.util.decoding.PixelBasedDecoder method) extract_barcodes_with_threshold() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) extract_refactors() (merlin.util.decoding.PixelBasedDecoder method)

F

FiducialCorrelationWarp (class in merlin.analysis.warp) figure_exists() (merlin.core.dataset.DataSet method) FilterBarcodes (class in merlin.analysis.filterbarcodes) flip_bit() (in module merlin.util.binary) fov_coordinates_to_global() (merlin.analysis.globalalign.CorrelationGlobalAlignment method) (merlin.analysis.globalalign.GlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) fov_global_extent() (merlin.analysis.globalalign.SimpleGlobalAlignment method) fov_scroll_update() (merlin.view.widgets.regionview.RegionViewWidget method) fov_to_global_transform() (merlin.analysis.globalalign.CorrelationGlobalAlignment method) (merlin.analysis.globalalign.GlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method)

fragment_count() (merlin.analysis.decode.Decode method) (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) (merlin.analysis.filterbarcodes.FilterBarcodes method) (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) (merlin.analysis.optimize.OptimizeIteration method) (merlin.analysis.preprocess.DeconvolutionPreprocess method) (merlin.analysis.warp.FiducialCorrelationWarp method) (merlin.core.analysistask.ParallelAnalysisTask method)

G

generate_analysis_tasks_and_snakefile() (in module merlin.merlin) GenerateAdaptiveThreshold (class in merlin.analysis.filterbarcodes) GenerateMosaic (class in merlin.analysis.generatemosaic) get_adaptive_thresholds() (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) get_aligned_image() (merlin.analysis.warp.Warp method) get_aligned_image_set() (merlin.analysis.warp.Warp method) get_analysis_complete_time() (merlin.core.dataset.DataSet method) get_analysis_datasets() (in module merlin) get_analysis_elapsed_time() (merlin.core.dataset.DataSet method) get_analysis_environment() (merlin.core.dataset.DataSet method) get_analysis_image() (merlin.core.dataset.DataSet method) get_analysis_image_set() (merlin.core.dataset.DataSet method) get_analysis_name() (merlin.core.analysistask.AnalysisTask method) get_analysis_start_time() (merlin.core.dataset.DataSet method) get_analysis_subdirectory() (merlin.core.dataset.DataSet method) get_analysis_tasks() (merlin.core.dataset.DataSet method) get_area_bins() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_backgrounds() (merlin.analysis.optimize.OptimizeIteration method) get_barcode_areas() (merlin.util.barcodedb.BarcodeDB method) get_barcode_count_history() (merlin.analysis.optimize.OptimizeIteration method) get_barcode_database() (merlin.analysis.decode.BarcodeSavingParallelAnalysisTask method) get_barcode_distances() (merlin.util.barcodedb.BarcodeDB method) get_barcode_intensities() (merlin.util.barcodedb.BarcodeDB method) get_barcodes() (merlin.util.barcodedb.BarcodeDB method) (merlin.util.barcodedb.PyTablesBarcodeDB method) get_blank_count_histogram() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_blank_fraction_histogram() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_chromatic_corrector() (merlin.analysis.optimize.OptimizeIteration method) get_codebook() (merlin.analysis.decode.Decode method) (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) (merlin.analysis.filterbarcodes.FilterBarcodes method) (merlin.analysis.optimize.OptimizeIteration method) (merlin.analysis.preprocess.DeconvolutionPreprocess method) (merlin.core.dataset.MERFISHDataSet method) get_codebooks() (merlin.core.dataset.MERFISHDataSet method) get_coding_count_histogram() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_cursor_position() (merlin.view.widgets.regionview.ImageViewSynchronizer method) get_data_organization() (merlin.core.dataset.MERFISHDataSet method) get_dependencies() (merlin.analysis.decode.Decode method) (merlin.analysis.exportbarcodes.ExportBarcodes method) (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) (merlin.analysis.filterbarcodes.FilterBarcodes method) (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) (merlin.analysis.generatemosaic.GenerateMosaic method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) (merlin.analysis.optimize.OptimizeIteration method) (merlin.analysis.plotperformance.PlotPerformance method) (merlin.analysis.preprocess.DeconvolutionPreprocess method) (merlin.analysis.warp.FiducialCorrelationWarp method) (merlin.core.analysistask.AnalysisTask method) get_distance_bins() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_estimated_memory() (merlin.analysis.decode.Decode method) (merlin.analysis.exportbarcodes.ExportBarcodes method) (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) (merlin.analysis.filterbarcodes.FilterBarcodes method) (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) (merlin.analysis.generatemosaic.GenerateMosaic method) (merlin.analysis.globalalign.CorrelationGlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) (merlin.analysis.optimize.OptimizeIteration method) (merlin.analysis.plotperformance.PlotPerformance method) (merlin.analysis.preprocess.DeconvolutionPreprocess method) (merlin.analysis.warp.FiducialCorrelationWarp method) (merlin.core.analysistask.AnalysisTask method)

get_estimated_time() (merlin.analysis.decode.Decode method) (merlin.analysis.exportbarcodes.ExportBarcodes method) (merlin.analysis.filterbarcodes.AdaptiveFilterBarcodes method) (merlin.analysis.filterbarcodes.FilterBarcodes method) (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) (merlin.analysis.generatemosaic.GenerateMosaic method) (merlin.analysis.globalalign.CorrelationGlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) (merlin.analysis.optimize.OptimizeIteration method) (merlin.analysis.plotperformance.PlotPerformance method) (merlin.analysis.preprocess.DeconvolutionPreprocess method) (merlin.analysis.warp.FiducialCorrelationWarp method) (merlin.core.analysistask.AnalysisTask method) get_fiducial_image() (merlin.core.dataset.MERFISHDataSet method) get_filtered_barcodes() (merlin.util.barcodedb.BarcodeDB method) (merlin.util.barcodedb.PyTablesBarcodeDB method) get_fov_offset() (merlin.core.dataset.MERFISHDataSet method) get_fovs() (merlin.core.dataset.MERFISHDataSet method) get_global_extent() (merlin.analysis.globalalign.CorrelationGlobalAlignment method) (merlin.analysis.globalalign.GlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) get_image_dimensions() (merlin.core.dataset.ImageDataSet method) get_image_file_names() (merlin.core.dataset.ImageDataSet method) get_image_xml_metadata() (merlin.core.dataset.ImageDataSet method) get_imaging_rounds() (merlin.core.dataset.MERFISHDataSet method) get_intensities_for_barcodes_with_area() (merlin.util.barcodedb.BarcodeDB method) (merlin.util.barcodedb.PyTablesBarcodeDB method) get_intensity_bins() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_log_subdirectory() (merlin.core.dataset.DataSet method) get_logger() (merlin.core.dataset.DataSet method) get_microns_per_pixel() (merlin.core.dataset.ImageDataSet method) get_mosaic() (merlin.analysis.generatemosaic.GenerateMosaic method) get_parameters() (merlin.core.analysistask.AnalysisTask method) get_pixel_histogram() (merlin.analysis.preprocess.Preprocess method) get_processed_image() (merlin.analysis.preprocess.DeconvolutionPreprocess method) get_processed_image_set() (merlin.analysis.preprocess.DeconvolutionPreprocess method) get_raw_image() (merlin.core.dataset.MERFISHDataSet method) get_reference_color() (merlin.analysis.optimize.OptimizeIteration method) get_scale_factor_history() (merlin.analysis.optimize.OptimizeIteration method) get_scale_factors() (merlin.analysis.optimize.OptimizeIteration method) get_selected_barcode() (merlin.view.widgets.regionview.ImageViewSynchronizer method) get_snakemake_path() (merlin.core.dataset.DataSet method) get_stage_positions() (merlin.core.dataset.MERFISHDataSet method) get_stored_codebook_name() (merlin.core.dataset.MERFISHDataSet method) get_task_subdirectory() (merlin.core.dataset.DataSet method) get_total_count_histogram() (merlin.analysis.filterbarcodes.GenerateAdaptiveThreshold method) get_transform() (merlin.view.widgets.regionview.ImageViewSynchronizer method) get_transformation() (merlin.analysis.warp.Warp method) get_z_positions() (merlin.core.dataset.MERFISHDataSet method) global_coordinates_to_fov() (merlin.analysis.globalalign.GlobalAlignment method) (merlin.analysis.globalalign.SimpleGlobalAlignment method) GlobalAlignment (class in merlin.analysis.globalalign)

I

image_stack_size() (merlin.core.dataset.ImageDataSet method) ImageDataSet (class in merlin.core.dataset) ImageViewSynchronizer (class in merlin.view.widgets.regionview) IncompatibleVersionException int_to_bit_list() (in module merlin.util.binary) InternallyParallelAnalysisTask (class in merlin.core.analysistask) InvalidParameterException is_analysis_idle() (merlin.core.dataset.DataSet method) is_compatible() (in module merlin) is_complete() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method)

is_error() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method) is_parallel() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.InternallyParallelAnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method) is_running() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method) is_started() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method)

K

k_bit_set() (in module merlin.util.binary)

L

list_analysis_files() (merlin.core.dataset.DataSet method) load_analysis_task() (merlin.core.dataset.DataSet method) load_codebook() (merlin.core.dataset.MERFISHDataSet method) load_codebooks() (merlin.core.dataset.MERFISHDataSet method) load_dataframe_from_csv() (merlin.core.dataset.DataSet method)

load_image() (merlin.core.dataset.ImageDataSet method) load_json_analysis_result() (merlin.core.dataset.DataSet method) load_numpy_analysis_result() (merlin.core.dataset.DataSet method) load_numpy_analysis_result_if_available() (merlin.core.dataset.DataSet method) load_pickle_analysis_result() (merlin.core.dataset.DataSet method) LocalExecutor (class in merlin.core.executor)

M

MERFISHDataSet (class in merlin.core.dataset) merlin (module) merlin() (in module merlin.merlin) merlin.analysis (module), [1] merlin.analysis.decode (module) merlin.analysis.exportbarcodes (module) merlin.analysis.filterbarcodes (module) merlin.analysis.generatemosaic (module) merlin.analysis.globalalign (module) merlin.analysis.optimize (module) merlin.analysis.plotperformance (module) merlin.analysis.preprocess (module) merlin.analysis.warp (module) merlin.core (module), [1] merlin.core.analysistask (module)

merlin.core.dataset (module) merlin.core.executor (module) merlin.merlin (module) merlin.util (module), [1] merlin.util.barcodedb (module) merlin.util.binary (module) merlin.util.decoding (module) merlin.view (module), [1] merlin.view.merlinview (module) merlin.view.widgets (module) merlin.view.widgets.regionview (module) merlin_view() (in module merlin.view.merlinview) mouseMoveEvent() (merlin.view.widgets.regionview.RegionImageViewWidget method) mousePressEvent() (merlin.view.widgets.regionview.RegionImageViewWidget method) mouseReleaseEvent() (merlin.view.widgets.regionview.RegionImageViewWidget method)

N

normalize() (in module merlin.util.decoding)

O

open_hdf5_file() (merlin.core.dataset.DataSet method) open_pandas_hdfstore() (merlin.core.dataset.DataSet method)

open_table() (merlin.core.dataset.DataSet method) OptimizeIteration (class in merlin.analysis.optimize)

P

paintEvent() (merlin.view.widgets.regionview.RegionImageViewWidget method) ParallelAnalysisTask (class in merlin.core.analysistask) PixelBasedDecoder (class in merlin.util.decoding)

PlotPerformance (class in merlin.analysis.plotperformance) position_to_z_index() (merlin.core.dataset.MERFISHDataSet method) Preprocess (class in merlin.analysis.preprocess) PyTablesBarcodeDB (class in merlin.util.barcodedb)

R

record_analysis_complete() (merlin.core.dataset.DataSet method) record_analysis_error() (merlin.core.dataset.DataSet method) record_analysis_running() (merlin.core.dataset.DataSet method) record_analysis_started() (merlin.core.dataset.DataSet method) RegionImageViewWidget (class in merlin.view.widgets.regionview) RegionViewWidget (class in merlin.view.widgets.regionview)

reset_analysis_status() (merlin.core.dataset.DataSet method) run() (merlin.core.analysistask.AnalysisTask method) (merlin.core.analysistask.ParallelAnalysisTask method) (merlin.core.executor.Executor method) (merlin.core.executor.LocalExecutor method) run_with_snakemake() (in module merlin.merlin)

S

save() (merlin.core.analysistask.AnalysisTask method) save_analysis_task() (merlin.core.dataset.DataSet method) save_codebook() (merlin.core.dataset.MERFISHDataSet method) save_dataframe_to_csv() (merlin.core.dataset.DataSet method) save_figure() (merlin.core.dataset.DataSet method) save_json_analysis_result() (merlin.core.dataset.DataSet method) save_numpy_analysis_result() (merlin.core.dataset.DataSet method) save_numpy_txt_analysis_result() (merlin.core.dataset.DataSet method) save_pickle_analysis_result() (merlin.core.dataset.DataSet method)

save_workflow() (merlin.core.dataset.DataSet method) scale_image() (merlin.view.widgets.regionview.RegionImageViewWidget method) set_core_count() (merlin.core.analysistask.InternallyParallelAnalysisTask method) set_cursor_position() (merlin.view.widgets.regionview.ImageViewSynchronizer method) set_data() (merlin.view.widgets.regionview.RegionImageViewWidget method) set_fov() (merlin.view.widgets.regionview.RegionViewWidget method) set_selected_barcode() (merlin.view.widgets.regionview.ImageViewSynchronizer method) set_z_index() (merlin.view.widgets.regionview.RegionViewWidget method) SimpleGlobalAlignment (class in merlin.analysis.globalalign) store_env() (in module merlin)

U

updateViewSignal (merlin.view.widgets.regionview.ImageViewSynchronizer attribute)

V

version() (in module merlin)

W

Warp (class in merlin.analysis.warp) wheelEvent() (merlin.view.widgets.regionview.RegionImageViewWidget method)

write_barcodes() (merlin.util.barcodedb.BarcodeDB method) (merlin.util.barcodedb.PyTablesBarcodeDB method) writer_for_analysis_images() (merlin.core.dataset.DataSet method)

Z

z_index_to_position() (merlin.core.dataset.MERFISHDataSet method)

z_scroll_update() (merlin.view.widgets.regionview.RegionViewWidget method)