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Locan 0.22.0.dev32+g4bfc3ab8b
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Locan 0.22.0.dev32+g4bfc3ab8b

Getting started

  • Installation
  • Tutorials
    • LocData
    • Load localization data
    • Hulls
    • Metadata
    • Regions
    • Filter
    • Cluster
    • Render
    • Simulate
    • Track
    • Transform
    • Localizations per frame
    • Localization precision
    • Localization property
    • Blinking
    • Coordinate based colocalization
    • Drift
    • Local density
    • Nearest neighbor distances
    • Pair distances
    • Radial distance distribution
    • Ripley
    • Grouped cluster properties
    • How to use an analysis class
    • Analysis pipeline
    • Files
    • Multiprocessing
    • Datasets
    • Logging
    • Notebook execution table
  • Docker

User Guide

  • Package Design
    • Data structures
    • Metadata
    • Properties
    • Methods for data analysis
  • Command-line interface
  • Colormaps
  • User Interface

API Documentation

  • API Reference
    • locan.analysis
      • locan.analysis.accumulation_analysis
        • locan.analysis.accumulation_analysis.AccumulationClusterCheck
      • locan.analysis.blinking
        • locan.analysis.blinking.BlinkStatistics
      • locan.analysis.cbc
        • locan.analysis.cbc.CoordinateBasedColocalization
      • locan.analysis.convex_hull_expectation
        • locan.analysis.convex_hull_expectation.ConvexHullExpectation
        • locan.analysis.convex_hull_expectation.ConvexHullExpectationBatch
        • locan.analysis.convex_hull_expectation.ConvexHullExpectationResults
        • locan.analysis.convex_hull_expectation.ConvexHullExpectationValues
        • locan.analysis.convex_hull_expectation.ConvexHullProperty
        • locan.analysis.convex_hull_expectation.compute_convex_hull_region_measure_2d
      • locan.analysis.drift
        • locan.analysis.drift.Drift
        • locan.analysis.drift.DriftComponent
        • locan.analysis.drift.DriftModel
      • locan.analysis.grouped_property_expectation
        • locan.analysis.grouped_property_expectation.GroupedPropertyExpectation
        • locan.analysis.grouped_property_expectation.GroupedPropertyExpectationResults
      • locan.analysis.local_density
        • locan.analysis.local_density.LocalDensity
      • locan.analysis.localization_precision
        • locan.analysis.localization_precision.LocalizationPrecision
        • locan.analysis.localization_precision.PairwiseDistance1d
        • locan.analysis.localization_precision.PairwiseDistance1dIdenticalSigmaZeroMu
        • locan.analysis.localization_precision.PairwiseDistance2d
        • locan.analysis.localization_precision.PairwiseDistance2dIdenticalSigma
        • locan.analysis.localization_precision.PairwiseDistance2dIdenticalSigmaZeroMu
        • locan.analysis.localization_precision.PairwiseDistance3d
        • locan.analysis.localization_precision.PairwiseDistance3dIdenticalSigmaZeroMu
      • locan.analysis.localization_property
        • locan.analysis.localization_property.LocalizationProperty
      • locan.analysis.localization_property_2d
        • locan.analysis.localization_property_2d.FitImageResults
        • locan.analysis.localization_property_2d.LocalizationProperty2d
      • locan.analysis.localization_property_correlations
        • locan.analysis.localization_property_correlations.LocalizationPropertyCorrelations
      • locan.analysis.localizations_per_frame
        • locan.analysis.localizations_per_frame.LocalizationsPerFrame
      • locan.analysis.nearest_neighbor
        • locan.analysis.nearest_neighbor.NNDistances_csr_2d
        • locan.analysis.nearest_neighbor.NNDistances_csr_3d
        • locan.analysis.nearest_neighbor.NearestNeighborDistances
        • locan.analysis.nearest_neighbor.pdf_nnDistances_csr_2D
        • locan.analysis.nearest_neighbor.pdf_nnDistances_csr_3D
      • locan.analysis.pair_distances
        • locan.analysis.pair_distances.PairDistances
      • locan.analysis.pipeline
        • locan.analysis.pipeline.Pipeline
        • locan.analysis.pipeline.computation_test
      • locan.analysis.position_variance_expectation
        • locan.analysis.position_variance_expectation.PositionVarianceExpectation
        • locan.analysis.position_variance_expectation.PositionVarianceExpectationResults
      • locan.analysis.radial_distribution
        • locan.analysis.radial_distribution.RadialDistribution
        • locan.analysis.radial_distribution.RadialDistributionBatch
        • locan.analysis.radial_distribution.RadialDistributionBatchResults
        • locan.analysis.radial_distribution.RadialDistributionResults
      • locan.analysis.ripley
        • locan.analysis.ripley.RipleysHFunction
        • locan.analysis.ripley.RipleysKFunction
        • locan.analysis.ripley.RipleysLFunction
        • locan.analysis.ripley.plot
      • locan.analysis.subpixel_bias
        • locan.analysis.subpixel_bias.SubpixelBias
      • locan.analysis.uncertainty
        • locan.analysis.uncertainty.LocalizationUncertainty
        • locan.analysis.uncertainty.localization_precision_model_1
        • locan.analysis.uncertainty.localization_precision_model_2
        • locan.analysis.uncertainty.localization_precision_model_3
    • locan.constants
      • locan.constants.ROOT_DIR
      • locan.constants.PROPERTY_KEYS
      • locan.constants.DECODE_KEYS
      • locan.constants.ELYRA_KEYS
      • locan.constants.NANOIMAGER_KEYS
      • locan.constants.RAPIDSTORM_KEYS
      • locan.constants.SMAP_KEYS
      • locan.constants.SMLM_KEYS
      • locan.constants.THUNDERSTORM_KEYS
      • locan.constants.FileType
      • locan.constants.HullType
      • locan.constants.PropertyDescription
      • locan.constants.PropertyKey
      • locan.constants.RenderEngine
    • locan.configuration
      • locan.configuration.DATASETS_DIR
      • locan.configuration.RENDER_ENGINE
      • locan.configuration.N_JOBS
      • locan.configuration.COLORMAP_DEFAULTS
      • locan.configuration.TQDM_LEAVE
      • locan.configuration.TQDM_DISABLE
    • locan.data
      • locan.data.hulls
        • locan.data.hulls.hull
          • locan.data.hulls.hull.BoundingBox
          • locan.data.hulls.hull.ConvexHull
          • locan.data.hulls.hull.OrientedBoundingBox
        • locan.data.hulls.alpha_shape
          • locan.data.hulls.alpha_shape.AlphaComplex
          • locan.data.hulls.alpha_shape.AlphaShape
      • locan.data.images
        • locan.data.images.ArrayApiObject
        • locan.data.images.Image
        • locan.data.images.ImageBase
        • locan.data.images.ImageProtocol
        • locan.data.images.PillowImage
        • locan.data.images.is_array_api_obj
      • locan.data.locdata
        • locan.data.locdata.LocData
      • locan.data.metadata_utils
        • locan.data.metadata_utils.load_metadata_from_toml
        • locan.data.metadata_utils.merge_metadata
        • locan.data.metadata_utils.message_scheme
        • locan.data.metadata_utils.metadata_from_toml_string
        • locan.data.metadata_utils.metadata_to_formatted_string
      • locan.data.regions
        • locan.data.regions.region
          • locan.data.regions.region.AxisOrientedCuboid
          • locan.data.regions.region.AxisOrientedHypercuboid
          • locan.data.regions.region.AxisOrientedRectangle
          • locan.data.regions.region.Cuboid
          • locan.data.regions.region.Ellipse
          • locan.data.regions.region.EmptyRegion
          • locan.data.regions.region.Interval
          • locan.data.regions.region.LineSegment2D
          • locan.data.regions.region.LineSegment3D
          • locan.data.regions.region.MultiPolygon
          • locan.data.regions.region.Polygon
          • locan.data.regions.region.Rectangle
          • locan.data.regions.region.Region
          • locan.data.regions.region.Region1D
          • locan.data.regions.region.Region2D
          • locan.data.regions.region.Region3D
          • locan.data.regions.region.RegionND
          • locan.data.regions.region.RoiRegion
          • locan.data.regions.region.get_region_from_open3d
          • locan.data.regions.region.get_region_from_shapely
        • locan.data.regions.region_utils
          • locan.data.regions.region_utils.expand_region
          • locan.data.regions.region_utils.get_region_from_intervals
          • locan.data.regions.region_utils.regions_union
          • locan.data.regions.region_utils.surrounding_region
      • locan.data.validation
        • locan.data.validation.Collection
    • locan.datasets
      • locan.datasets.load_npc
      • locan.datasets.load_tubulin
    • locan.dependencies
      • locan.dependencies.INSTALL_REQUIRES
      • locan.dependencies.EXTRAS_REQUIRE
      • locan.dependencies.IMPORT_NAMES
      • locan.dependencies.HAS_DEPENDENCY
      • locan.dependencies.QtBindings
      • locan.dependencies.needs_package
      • locan.dependencies.needs_package_version
    • locan.gui
      • locan.gui.io
        • locan.gui.io.file_dialog
        • locan.gui.io.set_file_path_dialog
    • locan.locan_io
      • locan.locan_io.files
        • locan.locan_io.files.Files
      • locan.locan_io.locdata
        • locan.locan_io.locdata.io_locdata
          • locan.locan_io.locdata.io_locdata.load_locdata
          • locan.locan_io.locdata.io_locdata.load_txt_file
        • locan.locan_io.locdata.utilities
          • locan.locan_io.locdata.utilities.convert_property_names
          • locan.locan_io.locdata.utilities.convert_property_types
          • locan.locan_io.locdata.utilities.open_path_or_file_like
        • locan.locan_io.locdata.rapidstorm_io
          • locan.locan_io.locdata.rapidstorm_io.load_rapidSTORM_file
          • locan.locan_io.locdata.rapidstorm_io.load_rapidSTORM_header
          • locan.locan_io.locdata.rapidstorm_io.load_rapidSTORM_track_file
          • locan.locan_io.locdata.rapidstorm_io.load_rapidSTORM_track_header
        • locan.locan_io.locdata.thunderstorm_io
          • locan.locan_io.locdata.thunderstorm_io.load_thunderstorm_file
          • locan.locan_io.locdata.thunderstorm_io.load_thunderstorm_header
          • locan.locan_io.locdata.thunderstorm_io.save_thunderstorm_csv
        • locan.locan_io.locdata.elyra_io
          • locan.locan_io.locdata.elyra_io.load_Elyra_file
          • locan.locan_io.locdata.elyra_io.load_Elyra_header
        • locan.locan_io.locdata.nanoimager_io
          • locan.locan_io.locdata.nanoimager_io.load_Nanoimager_file
          • locan.locan_io.locdata.nanoimager_io.load_Nanoimager_header
        • locan.locan_io.locdata.asdf_io
          • locan.locan_io.locdata.asdf_io.load_asdf_file
          • locan.locan_io.locdata.asdf_io.save_asdf
        • locan.locan_io.locdata.smlm_io
          • locan.locan_io.locdata.smlm_io.load_SMLM_file
          • locan.locan_io.locdata.smlm_io.load_SMLM_header
          • locan.locan_io.locdata.smlm_io.load_SMLM_manifest
          • locan.locan_io.locdata.smlm_io.manifest_file_info_from_locdata
          • locan.locan_io.locdata.smlm_io.manifest_format_from_locdata
          • locan.locan_io.locdata.smlm_io.manifest_from_locdata
          • locan.locan_io.locdata.smlm_io.save_SMLM
        • locan.locan_io.locdata.decode_io
          • locan.locan_io.locdata.decode_io.load_decode_file
          • locan.locan_io.locdata.decode_io.load_decode_header
        • locan.locan_io.locdata.smap_io
          • locan.locan_io.locdata.smap_io.load_SMAP_file
          • locan.locan_io.locdata.smap_io.load_SMAP_header
          • locan.locan_io.locdata.smap_io.save_SMAP_csv
      • locan.locan_io.utilities
        • locan.locan_io.utilities.find_file_upstream
    • locan.process
      • locan.process.aggregate
        • locan.process.aggregate.Bins
        • locan.process.aggregate.histogram
        • locan.process.aggregate.is_array_like
      • locan.process.cluster
        • locan.process.cluster.clustering
          • locan.process.cluster.clustering.cluster_by_bin
          • locan.process.cluster.clustering.cluster_dbscan
          • locan.process.cluster.clustering.cluster_hdbscan
        • locan.process.cluster.utils
          • locan.process.cluster.utils.serial_clustering
      • locan.process.filter
        • locan.process.filter.Selector
        • locan.process.filter.exclude_sparse_points
        • locan.process.filter.filter_condition
        • locan.process.filter.localizations_in_cluster_regions
        • locan.process.filter.random_subset
        • locan.process.filter.select_by_condition
        • locan.process.filter.select_by_image_mask
        • locan.process.filter.select_by_region
      • locan.process.register
        • locan.process.register.Transformation
        • locan.process.register.register_cc
        • locan.process.register.register_icp
      • locan.process.properties
        • locan.process.properties.misc
          • locan.process.properties.misc.InertiaMoments
          • locan.process.properties.misc.distance_to_point
          • locan.process.properties.misc.distance_to_region
          • locan.process.properties.misc.distance_to_region_boundary
          • locan.process.properties.misc.inertia_moments
          • locan.process.properties.misc.max_distance
        • locan.process.properties.locdata_statistics
          • locan.process.properties.locdata_statistics.range_from_collection
          • locan.process.properties.locdata_statistics.ranges
          • locan.process.properties.locdata_statistics.statistics
      • locan.process.tracking
        • locan.process.tracking.link_locdata
        • locan.process.tracking.track
      • locan.process.transform
        • locan.process.transform.spatial
          • locan.process.transform.spatial.bunwarpj
            • locan.process.transform.spatial.bunwarpj.bunwarp
          • locan.process.transform.spatial.spatial_transformation
            • locan.process.transform.spatial.spatial_transformation.overlay
            • locan.process.transform.spatial.spatial_transformation.standardize
            • locan.process.transform.spatial.spatial_transformation.transform_affine
        • locan.process.transform.intensity_transformation
          • locan.process.transform.intensity_transformation.transform_counts_to_photons
    • locan.rois
      • locan.rois.roi
        • locan.rois.roi.Roi
        • locan.rois.roi.RoiLegacy_0
        • locan.rois.roi.load_locdata_from_roi_file
        • locan.rois.roi.rasterize
    • locan.scripts
      • locan.scripts.script_check
        • locan.scripts.script_check.main
        • locan.scripts.script_check.render_locs_per_frame_napari
        • locan.scripts.script_check.sc_check
      • locan.scripts.script_rois
        • locan.scripts.script_rois.main
        • locan.scripts.script_rois.sc_draw_roi_napari
      • locan.scripts.script_draw_roi
        • locan.scripts.script_draw_roi.main
        • locan.scripts.script_draw_roi.sc_draw_roi_mpl
      • locan.scripts.script_napari
        • locan.scripts.script_napari.main
        • locan.scripts.script_napari.sc_napari
      • locan.scripts.script_show_versions
        • locan.scripts.script_show_versions.main
      • locan.scripts.script_test
        • locan.scripts.script_test.main
    • locan.simulation
      • locan.simulation.simulate_locdata
        • locan.simulation.simulate_locdata.make_Matern
        • locan.simulation.simulate_locdata.make_NeymanScott
        • locan.simulation.simulate_locdata.make_Poisson
        • locan.simulation.simulate_locdata.make_Thomas
        • locan.simulation.simulate_locdata.make_cluster
        • locan.simulation.simulate_locdata.make_dstorm
        • locan.simulation.simulate_locdata.make_uniform
        • locan.simulation.simulate_locdata.randomize
        • locan.simulation.simulate_locdata.resample
        • locan.simulation.simulate_locdata.simulate_Matern
        • locan.simulation.simulate_locdata.simulate_NeymanScott
        • locan.simulation.simulate_locdata.simulate_Poisson
        • locan.simulation.simulate_locdata.simulate_Thomas
        • locan.simulation.simulate_locdata.simulate_cluster
        • locan.simulation.simulate_locdata.simulate_dstorm
        • locan.simulation.simulate_locdata.simulate_frame_numbers
        • locan.simulation.simulate_locdata.simulate_tracks
        • locan.simulation.simulate_locdata.simulate_uniform
      • locan.simulation.simulate_drift
        • locan.simulation.simulate_drift.add_drift
    • locan.tests
      • locan.tests.test
    • locan.utils
      • locan.utils.miscellaneous
        • locan.utils.miscellaneous.iterate_2d_array
      • locan.utils.statistics
        • locan.utils.statistics.WeightedMeanVariance
        • locan.utils.statistics.biased_variance
        • locan.utils.statistics.ratio_fwhm_to_sigma
        • locan.utils.statistics.weighted_mean_variance
      • locan.utils.system_information
        • locan.utils.system_information.dependency_info
        • locan.utils.system_information.show_versions
        • locan.utils.system_information.system_info
      • locan.utils.rotation
        • locan.utils.rotation.Rotation2D
        • locan.utils.rotation.Rotation3D
    • locan.visualize
      • locan.visualize.colormap
        • locan.visualize.colormap.colormap_registry
        • locan.visualize.colormap.Colormap
        • locan.visualize.colormap.Colormaps
        • locan.visualize.colormap.get_colormap
      • locan.visualize.render
        • locan.visualize.render.render_2d
        • locan.visualize.render.render_3d
      • locan.visualize.render_mpl
        • locan.visualize.render_mpl.render2d
          • locan.visualize.render_mpl.render2d.apply_window
          • locan.visualize.render_mpl.render2d.render_2d_mpl
          • locan.visualize.render_mpl.render2d.render_2d_rgb_mpl
          • locan.visualize.render_mpl.render2d.render_2d_scatter_density
          • locan.visualize.render_mpl.render2d.scatter_2d_mpl
          • locan.visualize.render_mpl.render2d.select_by_drawing_mpl
        • locan.visualize.render_mpl.render3d
          • locan.visualize.render_mpl.render3d.scatter_3d_mpl
      • locan.visualize.render_napari
        • locan.visualize.render_napari.render2d
          • locan.visualize.render_napari.render2d.render_2d_napari
          • locan.visualize.render_napari.render2d.render_2d_napari_image
          • locan.visualize.render_napari.render2d.render_2d_rgb_napari
        • locan.visualize.render_napari.render3d
          • locan.visualize.render_napari.render3d.render_3d_napari
          • locan.visualize.render_napari.render3d.render_3d_napari_image
          • locan.visualize.render_napari.render3d.render_3d_rgb_napari
        • locan.visualize.render_napari.utilities
          • locan.visualize.render_napari.utilities.get_rois
          • locan.visualize.render_napari.utilities.save_rois
          • locan.visualize.render_napari.utilities.select_by_drawing_napari
      • locan.visualize.transform
        • locan.visualize.transform.HistogramEqualization
        • locan.visualize.transform.Trafo
        • locan.visualize.transform.Transform
        • locan.visualize.transform.adjust_contrast

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locan.constants.HullType¶

class locan.constants.HullType(value)[source]¶

Bases: Enum

Hull definitions that are supported for LocData objects.

Attributes

BOUNDING_BOX

CONVEX_HULL

ORIENTED_BOUNDING_BOX

ALPHA_SHAPE

ALPHA_SHAPE = 'alpha_shape'¶
BOUNDING_BOX = 'bounding_box'¶
CONVEX_HULL = 'convex_hull'¶
ORIENTED_BOUNDING_BOX = 'oriented_bounding_box'¶
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locan.constants.PropertyDescription
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  • locan.constants.HullType
    • HullType
      • HullType.ALPHA_SHAPE
      • HullType.BOUNDING_BOX
      • HullType.CONVEX_HULL
      • HullType.ORIENTED_BOUNDING_BOX