Index

_

__call__() (sparcscore.pipeline.classification.CellFeaturizer method) (sparcscore.pipeline.classification.MLClusterClassifier method)

A

add_hdf_to_index() (sparcscore.ml.datasets.HDF5SingleCellDataset method) adjust_segmentation_indexes() (sparcscore.pipeline.segmentation.TimecourseSegmentation method)

autophagy_classifier1_0() (in module sparcscore.ml.pretrained_models) autophagy_classifier2_0() (in module sparcscore.ml.pretrained_models) autophagy_classifier2_1() (in module sparcscore.ml.pretrained_models)

B

BaseSegmentation (class in sparcscore.pipeline.workflows)

C

call_as_shard() (sparcscore.pipeline.segmentation.Segmentation method) (sparcscore.pipeline.segmentation.TimecourseSegmentation method) CellFeaturizer (class in sparcscore.pipeline.classification) ChannelReducer (class in sparcscore.ml.transforms) ChannelSelector (class in sparcscore.ml.transforms) classify() (sparcscore.pipeline.project.Project method) combine_datasets_balanced() (in module sparcscore.ml.utils)

configure_optimizers() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) confusion_plot() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) contact_filter() (in module sparcscore.processing.segmentation) contact_filter_lambda() (in module sparcscore.processing.segmentation) Cytosol_Cellpose_TimecourseSegmentation (class in sparcscore.pipeline.workflows) Cytosol_Cellpose_TimecourseSegmentation.CytosolSegmentationCellpose_Timecourse (class in sparcscore.pipeline.workflows) CytosolSegmentationCellpose (class in sparcscore.pipeline.workflows)

D

DAPISegmentation (class in sparcscore.pipeline.workflows) DAPISegmentationCellpose (class in sparcscore.pipeline.workflows) DEFAULT_CLASSIFICATION_DIR_NAME (sparcscore.pipeline.project.Project attribute) (sparcscore.pipeline.project.TimecourseProject attribute) DEFAULT_CONFIG_NAME (sparcscore.pipeline.project.Project attribute) (sparcscore.pipeline.project.TimecourseProject attribute) DEFAULT_EXTRACTION_DIR_NAME (sparcscore.pipeline.project.Project attribute) (sparcscore.pipeline.project.TimecourseProject attribute) DEFAULT_FILTER_FILE (sparcscore.pipeline.segmentation.Segmentation attribute) (sparcscore.pipeline.segmentation.ShardedSegmentation attribute) DEFAULT_FORMAT (sparcscore.pipeline.base.Logable attribute) DEFAULT_INPUT_IMAGE_NAME (sparcscore.pipeline.project.TimecourseProject attribute) (sparcscore.pipeline.segmentation.ShardedSegmentation attribute)

DEFAULT_LOG_NAME (sparcscore.pipeline.base.Logable attribute) DEFAULT_OUTPUT_FILE (sparcscore.pipeline.segmentation.Segmentation attribute) (sparcscore.pipeline.segmentation.ShardedSegmentation attribute) DEFAULT_SEGMENTATION_DIR_NAME (sparcscore.pipeline.project.Project attribute) (sparcscore.pipeline.project.TimecourseProject attribute) DEFAULT_SELECTION_DIR_NAME (sparcscore.pipeline.project.Project attribute) (sparcscore.pipeline.project.TimecourseProject attribute) DEFAULT_SHARD_FOLDER (sparcscore.pipeline.segmentation.ShardedSegmentation attribute) dir_labels (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) dir_list (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) directory (sparcscore.pipeline.base.Logable attribute) download_testimage() (in module sparcscore.processing.utils)

E

extract() (sparcscore.pipeline.project.Project method) (sparcscore.pipeline.project.TimecourseProject method)

F

flatten() (in module sparcscore.processing.utils)

forward() (sparcscore.ml.plmodels.MultilabelSupervisedModel method)

G

GaussianBlur (class in sparcscore.ml.transforms) GaussianNoise (class in sparcscore.ml.transforms) get_directory() (sparcscore.pipeline.base.ProcessingStep method)

get_timestamp() (sparcscore.pipeline.base.Logable method) getitem() (sparcscore.ml.datasets.HDF5SingleCellDataset method) global_otsu() (in module sparcscore.processing.segmentation)

H

HDF5CellExtraction (class in sparcscore.pipeline.extraction)

HDF5SingleCellDataset (class in sparcscore.ml.datasets)

I

identifier (sparcscore.pipeline.segmentation.Segmentation attribute) initialize_as_shard() (sparcscore.pipeline.segmentation.Segmentation method) (sparcscore.pipeline.segmentation.TimecourseSegmentation method)

input_path (sparcscore.pipeline.segmentation.Segmentation attribute)

L

len() (sparcscore.ml.datasets.HDF5SingleCellDataset method) LMDSelection (class in sparcscore.pipeline.selection) load_input_from_array() (sparcscore.pipeline.project.Project method) (sparcscore.pipeline.project.TimecourseProject method) load_input_from_file() (sparcscore.pipeline.project.Project method)

load_input_from_files() (sparcscore.pipeline.project.TimecourseProject method) load_input_from_files_and_merge() (sparcscore.pipeline.project.TimecourseProject method) load_maps_from_disk() (sparcscore.pipeline.segmentation.Segmentation method) log() (sparcscore.pipeline.base.Logable method) Logable (class in sparcscore.pipeline.base)

M

make_layers() (sparcscore.ml.models.VGGBase method) make_layers_MLP() (sparcscore.ml.models.VGGBase method) max_level (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) method (sparcscore.pipeline.workflows.Cytosol_Cellpose_TimecourseSegmentation attribute) (sparcscore.pipeline.workflows.Cytosol_Cellpose_TimecourseSegmentation.CytosolSegmentationCellpose_Timecourse attribute) (sparcscore.pipeline.workflows.Multithreaded_Cytosol_Cellpose_TimecourseSegmentation attribute) (sparcscore.pipeline.workflows.Multithreaded_Cytosol_Cellpose_TimecourseSegmentation.CytosolSegmentationCellpose_Timecourse attribute) (sparcscore.pipeline.workflows.MultithreadedWGATimecourseSegmentation attribute) (sparcscore.pipeline.workflows.MultithreadedWGATimecourseSegmentation.WGASegmentation_Timecourse attribute) (sparcscore.pipeline.workflows.ShardedCytosolSegmentationCellpose attribute) (sparcscore.pipeline.workflows.ShardedDAPISegmentation attribute) (sparcscore.pipeline.workflows.ShardedDAPISegmentationCellpose attribute) (sparcscore.pipeline.workflows.ShardedWGASegmentation attribute) (sparcscore.pipeline.workflows.WGATimecourseSegmentation attribute) (sparcscore.pipeline.workflows.WGATimecourseSegmentation.WGASegmentation_Timecourse attribute) MinMax() (in module sparcscore.processing.preprocessing)

MLClusterClassifier (class in sparcscore.pipeline.classification) module sparcscore.ml.datasets sparcscore.ml.metrics sparcscore.ml.pretrained_models sparcscore.ml.transforms sparcscore.ml.utils sparcscore.pipeline.workflows sparcscore.processing.preprocessing sparcscore.processing.segmentation sparcscore.processing.utils MultilabelSupervisedModel (class in sparcscore.ml.plmodels) Multithreaded_Cytosol_Cellpose_TimecourseSegmentation (class in sparcscore.pipeline.workflows) Multithreaded_Cytosol_Cellpose_TimecourseSegmentation.CytosolSegmentationCellpose_Timecourse (class in sparcscore.pipeline.workflows) MultithreadedSegmentation (class in sparcscore.pipeline.segmentation) MultithreadedWGATimecourseSegmentation (class in sparcscore.pipeline.workflows) MultithreadedWGATimecourseSegmentation.WGASegmentation_Timecourse (class in sparcscore.pipeline.workflows)

N

network (sparcscore.ml.plmodels.MultilabelSupervisedModel attribute)

numba_mask_centroid() (in module sparcscore.processing.segmentation)

O

on_train_epoch_end() (sparcscore.ml.plmodels.MultilabelSupervisedModel method)

on_validation_epoch_end() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) origins_from_distance() (in module sparcscore.processing.preprocessing)

P

percentile_normalization() (in module sparcscore.processing.preprocessing) plot_image() (in module sparcscore.processing.utils) precision() (in module sparcscore.ml.metrics) PRINT_MAPS_ON_DEBUG (sparcscore.pipeline.segmentation.Segmentation attribute)

process() (sparcscore.pipeline.extraction.HDF5CellExtraction method) (sparcscore.pipeline.extraction.TimecourseHDF5CellExtraction method) (sparcscore.pipeline.selection.LMDSelection method) ProcessingStep (class in sparcscore.pipeline.base) Project (class in sparcscore.pipeline.project)

R

RandomRotation (class in sparcscore.ml.transforms) recall() (in module sparcscore.ml.metrics) register_parameter() (sparcscore.pipeline.base.ProcessingStep method) remove_classes() (in module sparcscore.processing.segmentation)

resolve_sharding() (sparcscore.pipeline.segmentation.ShardedSegmentation method) return_fake_id (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) return_id (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) rolling_window_mean() (in module sparcscore.processing.preprocessing) root_dir (sparcscore.ml.datasets.HDF5SingleCellDataset attribute)

S

save_map() (sparcscore.pipeline.segmentation.Segmentation method) save_segmentation() (sparcscore.pipeline.segmentation.Segmentation method) (sparcscore.pipeline.segmentation.TimecourseSegmentation method) save_segmentation_zarr() (sparcscore.pipeline.segmentation.Segmentation method) scan_directory() (sparcscore.ml.datasets.HDF5SingleCellDataset method) segment() (sparcscore.pipeline.project.Project method) (sparcscore.pipeline.project.TimecourseProject method) segment_global_threshold() (in module sparcscore.processing.segmentation) segment_local_threshold() (in module sparcscore.processing.segmentation) Segmentation (class in sparcscore.pipeline.segmentation) select() (sparcscore.pipeline.project.Project method) select_channel (sparcscore.ml.datasets.HDF5SingleCellDataset attribute) ShardedCytosolSegmentationCellpose (class in sparcscore.pipeline.workflows) ShardedDAPISegmentation (class in sparcscore.pipeline.workflows) ShardedDAPISegmentationCellpose (class in sparcscore.pipeline.workflows) ShardedSegmentation (class in sparcscore.pipeline.segmentation) ShardedWGASegmentation (class in sparcscore.pipeline.workflows) shift_labels() (in module sparcscore.processing.segmentation) size_filter() (in module sparcscore.processing.segmentation)

sparcscore.ml.datasets module sparcscore.ml.metrics module sparcscore.ml.pretrained_models module sparcscore.ml.transforms module sparcscore.ml.utils module sparcscore.pipeline.workflows module sparcscore.processing.preprocessing module sparcscore.processing.segmentation module sparcscore.processing.utils module stats() (sparcscore.ml.datasets.HDF5SingleCellDataset method)

T

test_epoch_end() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) test_metrics (sparcscore.ml.plmodels.MultilabelSupervisedModel attribute) test_step() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) TimecourseHDF5CellExtraction (class in sparcscore.pipeline.extraction)

TimecourseProject (class in sparcscore.pipeline.project) TimecourseSegmentation (class in sparcscore.pipeline.segmentation) train_metrics (sparcscore.ml.plmodels.MultilabelSupervisedModel attribute) training_step() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) transform (sparcscore.ml.datasets.HDF5SingleCellDataset attribute)

V

val_metrics (sparcscore.ml.plmodels.MultilabelSupervisedModel attribute) validation_step() (sparcscore.ml.plmodels.MultilabelSupervisedModel method) VGG1 (class in sparcscore.ml.models)

VGG2 (class in sparcscore.ml.models) VGGBase (class in sparcscore.ml.models) visualize_class() (in module sparcscore.processing.utils)

W

WGASegmentation (class in sparcscore.pipeline.workflows) WGATimecourseSegmentation (class in sparcscore.pipeline.workflows)

WGATimecourseSegmentation.WGASegmentation_Timecourse (class in sparcscore.pipeline.workflows) window (sparcscore.pipeline.segmentation.Segmentation attribute)