Index _ | A | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W _ __call__() (scportrait.pipeline.featurization.CellFeaturizer method) (scportrait.pipeline.featurization.MLClusterClassifier method) A autophagy_classifier() (in module scportrait.tools.ml.pretrained_models) C calculate_chunk_sizes() (in module scportrait.io.daskmmap) calculate_chunk_sizes_chunks() (in module scportrait.io.daskmmap) CellFeaturizer (class in scportrait.pipeline.featurization) ChannelReducer (class in scportrait.tools.ml.transforms) ChannelSelector (class in scportrait.tools.ml.transforms) combine_datasets_balanced() (in module scportrait.tools.ml.utils) CombinedPhenixParser (class in scportrait.tools.parse._parse_phenix) complete_segmentation() (scportrait.pipeline.project.Project method) (scportrait.pipeline.segmentation.ShardedSegmentation method) config (scportrait.pipeline.project.Project attribute) configure_optimizers() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] confusion_plot() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) cyto_seg_name (scportrait.pipeline.project.Project attribute) CytosolOnlySegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) CytosolOnlySegmentationDownsamplingCellpose (class in scportrait.pipeline.segmentation.workflows) CytosolSegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) CytosolSegmentationDownsamplingCellpose (class in scportrait.pipeline.segmentation.workflows) D DAPISegmentation (class in scportrait.pipeline.segmentation.workflows) DAPISegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) dask_array_from_path() (in module scportrait.io.daskmmap) DEFAULT_DATA_LOADER (scportrait.pipeline.featurization.MLClusterClassifier attribute) DEFAULT_FILTER_ADDTIONAL_FILE (scportrait.pipeline.segmentation.Segmentation attribute) DEFAULT_IMAGE_DTYPE (scportrait.pipeline.project.Project attribute) DEFAULT_MODEL_CLASS (scportrait.pipeline.featurization.MLClusterClassifier attribute) DEFAULT_SEGMENTATION_DTYPE (scportrait.pipeline.project.Project attribute) DEFAULT_SINGLE_CELL_IMAGE_DTYPE (scportrait.pipeline.project.Project attribute) dir_labels (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) dir_list (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) F filehander (scportrait.pipeline.project.Project attribute) forward() (scportrait.tools.ml.models.VGGBase method) (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] G GaussianBlur (class in scportrait.tools.ml.transforms) GaussianNoise (class in scportrait.tools.ml.transforms) generate_thumbnail() (scportrait.tools.stitch._stitch.Stitcher method) get_data_dir() (in module scportrait.tools.ml.pretrained_models) get_stitching_information() (scportrait.tools.stitch._stitch.Stitcher method) getitem() (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method) H HDF5CellExtraction (class in scportrait.pipeline.extraction) HDF5SingleCellDataset (class in scportrait.tools.ml.datasets) I identifier (scportrait.pipeline.segmentation.Segmentation attribute) index_list (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) input_path (scportrait.pipeline.segmentation.Segmentation attribute) L label_colum (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) label_column_transform (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) label_dtype (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) LabelledHDF5SingleCellDataset (class in scportrait.tools.ml.datasets) len() (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method) LMDSelection (class in scportrait.pipeline.selection) load_hdf5_chunk() (in module scportrait.io.daskmmap) load_hdf5_contigious() (in module scportrait.io.daskmmap) load_input_from_array() (scportrait.pipeline.project.Project method) load_input_from_omezarr() (scportrait.pipeline.project.Project method) load_input_from_sdata() (scportrait.pipeline.project.Project method) load_input_from_tif_files() (scportrait.pipeline.project.Project method) load_multilabelSupervised() (in module scportrait.tools.ml.pretrained_models) M make_layers() (scportrait.tools.ml.models.VGGBase method) make_layers_MLP() (scportrait.tools.ml.models.VGGBase method) maps (scportrait.pipeline.segmentation.Segmentation attribute) max_level (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) method (scportrait.pipeline.segmentation.workflows.ShardedCytosolOnlySegmentationCellpose attribute) (scportrait.pipeline.segmentation.workflows.ShardedCytosolOnlySegmentationDownsamplingCellpose attribute) (scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationCellpose attribute) (scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationDownsamplingCellpose attribute) (scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentation attribute) (scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentationCellpose attribute) (scportrait.pipeline.segmentation.workflows.ShardedWGASegmentation attribute) MLClusterClassifier (class in scportrait.pipeline.featurization) mmap_dask_array_chunked() (in module scportrait.io.daskmmap) mmap_dask_array_contigious() (in module scportrait.io.daskmmap) module scportrait.io.daskmmap scportrait.io.read scportrait.pipeline.project scportrait.pipeline.segmentation.workflows scportrait.processing.images scportrait.processing.masks scportrait.tools.ml.datasets scportrait.tools.ml.metrics scportrait.tools.ml.pretrained_models scportrait.tools.ml.transforms scportrait.tools.ml.utils scportrait.tools.parse._parse_phenix scportrait.tools.stitch._stitch MultilabelSupervisedModel (class in scportrait.tools.ml.plmodels) N network (scportrait.tools.ml.plmodels.MultilabelSupervisedModel attribute) nuc_seg_name (scportrait.pipeline.project.Project attribute) O on_train_epoch_end() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) on_validation_epoch_end() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) P ParallelStitcher (class in scportrait.tools.stitch._stitch) parse() (scportrait.tools.parse._parse_phenix.PhenixParser method) PhenixParser (class in scportrait.tools.parse._parse_phenix) plot_qc() (scportrait.tools.stitch._stitch.Stitcher method) precision() (in module scportrait.tools.ml.metrics) PRINT_MAPS_ON_DEBUG (scportrait.pipeline.segmentation.Segmentation attribute) print_project_status() (scportrait.pipeline.project.Project method) process() (scportrait.pipeline.extraction.HDF5CellExtraction method) (scportrait.pipeline.featurization.CellFeaturizer method) (scportrait.pipeline.featurization.MLClusterClassifier method) (scportrait.pipeline.segmentation.Segmentation method) (scportrait.pipeline.segmentation.ShardedSegmentation method) (scportrait.pipeline.selection.LMDSelection method) Project (class in scportrait.pipeline.project) R RandomRotation (class in scportrait.tools.ml.transforms) read_ome_zarr() (in module scportrait.io.read) recall() (in module scportrait.tools.ml.metrics) return_fake_id (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) return_id (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) S save_map() (scportrait.pipeline.segmentation.Segmentation method) save_positions() (scportrait.tools.stitch._stitch.Stitcher method) scportrait.io.daskmmap module scportrait.io.read module scportrait.pipeline.project module scportrait.pipeline.segmentation.workflows module scportrait.processing.images module scportrait.processing.masks module scportrait.tools.ml.datasets module scportrait.tools.ml.metrics module scportrait.tools.ml.pretrained_models module scportrait.tools.ml.transforms module scportrait.tools.ml.utils module scportrait.tools.parse._parse_phenix module scportrait.tools.stitch._stitch module sdata_path (scportrait.pipeline.project.Project attribute) Segmentation (class in scportrait.pipeline.segmentation) select() (scportrait.pipeline.project.Project method) select_channel (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) ShardedCytosolOnlySegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) ShardedCytosolOnlySegmentationDownsamplingCellpose (class in scportrait.pipeline.segmentation.workflows) ShardedCytosolSegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) ShardedCytosolSegmentationDownsamplingCellpose (class in scportrait.pipeline.segmentation.workflows) ShardedDAPISegmentation (class in scportrait.pipeline.segmentation.workflows) ShardedDAPISegmentationCellpose (class in scportrait.pipeline.segmentation.workflows) ShardedSegmentation (class in scportrait.pipeline.segmentation) ShardedWGASegmentation (class in scportrait.pipeline.segmentation.workflows) sort_timepoints() (scportrait.tools.parse._parse_phenix.PhenixParser method) sort_wells() (scportrait.tools.parse._parse_phenix.PhenixParser method) split_dataset_fractions() (in module scportrait.tools.ml.utils) stats() (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method) stitch() (scportrait.tools.stitch._stitch.Stitcher method) Stitcher (class in scportrait.tools.stitch._stitch) T test_epoch_end() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) test_metrics (scportrait.tools.ml.plmodels.MultilabelSupervisedModel attribute) test_step() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] train_metrics (scportrait.tools.ml.plmodels.MultilabelSupervisedModel attribute) training_step() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] transform (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) U update_featurization_f() (scportrait.pipeline.project.Project method) V val_metrics (scportrait.tools.ml.plmodels.MultilabelSupervisedModel attribute) validation_step() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] VGG1 (class in scportrait.tools.ml.models) VGG2 (class in scportrait.tools.ml.models) VGGBase (class in scportrait.tools.ml.models) view_sdata() (scportrait.pipeline.project.Project method) W WGASegmentation (class in scportrait.pipeline.segmentation.workflows) window (scportrait.pipeline.segmentation.Segmentation attribute) write_ome_zarr() (scportrait.tools.stitch._stitch.Stitcher method) write_spatialdata() (scportrait.tools.stitch._stitch.Stitcher method) write_thumbnail() (scportrait.tools.stitch._stitch.Stitcher method) write_tif() (scportrait.tools.stitch._stitch.Stitcher method) write_tif_parallel() (scportrait.tools.stitch._stitch.ParallelStitcher method)
