Index _ | A | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W _ __call__() (scportrait.pipeline.classification.CellFeaturizer method) (scportrait.pipeline.classification.MLClusterClassifier method) A assemble_mosaic() (scportrait.tools.stitch._stitch.ParallelStitcher method) (scportrait.tools.stitch._stitch.Stitcher method) 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.classification) ChannelReducer (class in scportrait.tools.ml.transforms) ChannelSelector (class in scportrait.tools.ml.transforms) clear_cache() (scportrait.tools.stitch._stitch.Stitcher method) combine_datasets_balanced() (in module scportrait.tools.ml.utils) CombinedPhenixParser (class in scportrait.tools.parse._parse_phenix) complete_segmentation() (scportrait.pipeline.segmentation.ShardedSegmentation method) configure_optimizers() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] confusion_plot() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) copy_files() (scportrait.tools.parse._parse_phenix.PhenixParser method) create_cache() (scportrait.tools.stitch._stitch.Stitcher method) CytosolOnly_Segmentation_Downsampling_Cellpose (class in scportrait.pipeline.segmentation.workflows) CytosolOnlySegmentationCellpose (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.classification.MLClusterClassifier attribute) DEFAULT_FILTER_ADDTIONAL_FILE (scportrait.pipeline.segmentation.Segmentation attribute) DEFAULT_IMAGE_DTYPE (scportrait.pipeline.project.Project attribute) DEFAULT_MODEL_CLASS (scportrait.pipeline.classification.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 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_channel_info() (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) initialize_aligner() (scportrait.tools.stitch._stitch.ParallelStitcher method) (scportrait.tools.stitch._stitch.Stitcher method) initialize_mosaic() (scportrait.tools.stitch._stitch.ParallelStitcher method) (scportrait.tools.stitch._stitch.Stitcher method) initialize_outdir() (scportrait.tools.stitch._stitch.Stitcher method) initialize_reader() (scportrait.tools.stitch._stitch.Stitcher method) 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_sdata() (scportrait.pipeline.project.Project method) load_input_from_tif_files() (scportrait.pipeline.project.Project method) 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.Sharded_CytosolOnly_Cellpose_Segmentation attribute) (scportrait.pipeline.segmentation.workflows.Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose 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.classification) 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.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) 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) perform_alignment() (scportrait.tools.stitch._stitch.Stitcher 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) process() (scportrait.pipeline.classification.CellFeaturizer method) (scportrait.pipeline.classification.MLClusterClassifier method) (scportrait.pipeline.extraction.HDF5CellExtraction method) (scportrait.pipeline.segmentation.Segmentation method) (scportrait.pipeline.segmentation.ShardedSegmentation method) (scportrait.pipeline.segmentation.workflows.CytosolOnly_Segmentation_Downsampling_Cellpose method) (scportrait.pipeline.segmentation.workflows.CytosolSegmentationCellpose method) (scportrait.pipeline.segmentation.workflows.CytosolSegmentationDownsamplingCellpose method) (scportrait.pipeline.segmentation.workflows.DAPISegmentation method) (scportrait.pipeline.segmentation.workflows.DAPISegmentationCellpose method) (scportrait.pipeline.segmentation.workflows.WGASegmentation 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) reorder_channels() (scportrait.tools.stitch._stitch.Stitcher method) 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.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 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) setup_rescaling() (scportrait.tools.stitch._stitch.Stitcher method) Sharded_CytosolOnly_Cellpose_Segmentation (class in scportrait.pipeline.segmentation.workflows) Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose (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_classification_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) 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)
