Index

_

__getitem__() (scportrait.tools.ml.datasets.H5ScSingleCellDataset method) (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method)

__len__() (scportrait.tools.ml.datasets.H5ScSingleCellDataset method) (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method)

A

add_element_sdata() (in module scportrait.tools.spdata)

autophagy_classifier() (in module scportrait.tools.ml.pretrained_models)

C

cell_grid() (in module scportrait.plotting) cell_grid_multi_channel() (in module scportrait.plotting) cell_grid_single_channel() (in module scportrait.plotting) CellFeaturizer (class in scportrait.pipeline.featurization) CellFeaturizer_single_channel (class in scportrait.pipeline.featurization) ChannelMultiplier (class in scportrait.tools.ml.transforms) ChannelSelector (class in scportrait.tools.ml.transforms) check_for_missing_files() (scportrait.tools.parse.PhenixParser method) check_for_unassigned_cytosols() (scportrait.processing.masks.MatchNucleusCytosolIds method) CLEAN_LOG (scportrait.pipeline.featurization.ConvNeXtFeaturizer attribute) cleanup_filtering_lists() (scportrait.processing.masks.MatchNucleusCytosolIds method) cleanup_lookup_dictionary() (scportrait.processing.masks.MatchNucleusCytosolIds method) combine_datasets_balanced() (in module scportrait.tools.ml.utils)

CombinedPhenixParser (class in scportrait.tools.parse) complete_segmentation() (scportrait.pipeline.project.Project method) config (scportrait.pipeline.project.Project attribute) configure_optimizers() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method), [1] confusion_plot() (scportrait.tools.ml.plmodels.MultilabelSupervisedModel method) ConvNeXtFeaturizer (class in scportrait.pipeline.featurization) count_cytosol_occurances() (scportrait.processing.masks.MatchNucleusCytosolIds method) cyto_seg_name (scportrait.pipeline.project.Project attribute) cytosol_discard_list (scportrait.processing.masks.MatchNucleusCytosolIds attribute) cytosol_mask (scportrait.processing.masks.MatchNucleusCytosolIds 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) DEFAULT_IMAGE_DTYPE (scportrait.pipeline.project.Project 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.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute)

dir_list (scportrait.tools.ml.datasets.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) downsample (scportrait.processing.masks.MatchNucleusCytosolIds attribute) downsample_img_padding() (in module scportrait.processing.images) downsampling_factor (scportrait.processing.masks.MatchNucleusCytosolIds attribute)

E

EDF() (in module scportrait.processing.images) EnsembleClassifier (class in scportrait.pipeline.featurization)

erosion_dilation (scportrait.processing.masks.MatchNucleusCytosolIds attribute) extract() (scportrait.pipeline.project.Project method)

F

filehander (scportrait.pipeline.project.Project attribute) filter() (scportrait.processing.masks.MatchNucleusCytosolIds method), [1] (scportrait.processing.masks.SizeFilter method)

filtering_threshold (scportrait.processing.masks.MatchNucleusCytosolIds 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_composite() (in module scportrait.plotting) generate_lookup_table() (scportrait.processing.masks.MatchNucleusCytosolIds method) generate_metadata() (scportrait.tools.parse.PhenixParser method)

generate_thumbnail() (scportrait.tools.stitch.Stitcher method) get_data_dir() (in module scportrait.tools.ml.pretrained_models) get_datasets_to_combine() (scportrait.tools.parse.CombinedPhenixParser method) get_image_with_cellid() (in module scportrait.tools.h5sc) get_lookup_table() (scportrait.processing.masks.MatchNucleusCytosolIds method) get_stitching_information() (scportrait.tools.stitch.Stitcher method)

H

H5ScSingleCellDataset (class in scportrait.tools.ml.datasets)

HDF5CellExtraction (class in scportrait.pipeline.extraction) HDF5SingleCellDataset (class in scportrait.tools.ml.datasets)

I

identify_multinucleated_cells() (scportrait.processing.masks.MatchNucleusCytosolIds method) index_list (scportrait.tools.ml.datasets.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute)

initialize_lookup_table() (scportrait.processing.masks.MatchNucleusCytosolIds method)

L

label_column (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) label_column_transform (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) label_dtype (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) LabelledH5ScSingleCellDataset (class in scportrait.tools.ml.datasets) LabelledHDF5SingleCellDataset (class in scportrait.tools.ml.datasets) LMDSelection (class in scportrait.pipeline.selection)

load_input_from_array() (scportrait.pipeline.project.Project method) load_input_from_dask() (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_mask() (scportrait.processing.masks.SizeFilter method) load_masks() (scportrait.processing.masks.MatchNucleusCytosolIds 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) match_nucleus_id() (scportrait.processing.masks.MatchNucleusCytosolIds method) MatchNucleusCytosolIds (class in scportrait.processing.masks) max_level (scportrait.tools.ml.datasets.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute) maximum_intensity_projection() (in module scportrait.processing.images) 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)

module scportrait.io scportrait.pipeline.project scportrait.pipeline.segmentation.workflows scportrait.plotting scportrait.processing.images scportrait.processing.masks scportrait.tools.h5sc scportrait.tools.ml.datasets scportrait.tools.ml.metrics scportrait.tools.ml.pretrained_models scportrait.tools.ml.transforms scportrait.tools.ml.utils scportrait.tools.parse scportrait.tools.spdata scportrait.tools.spdata.pp scportrait.tools.stitch MultilabelSupervisedModel (class in scportrait.tools.ml.plmodels)

N

network (scportrait.tools.ml.plmodels.MultilabelSupervisedModel attribute) nuc_seg_name (scportrait.pipeline.project.Project attribute)

nuclei_discard_list (scportrait.processing.masks.MatchNucleusCytosolIds attribute) nucleus_lookup_dict (scportrait.processing.masks.MatchNucleusCytosolIds attribute) nucleus_mask (scportrait.processing.masks.MatchNucleusCytosolIds 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) parse() (scportrait.tools.parse.PhenixParser method) percentile_normalization() (in module scportrait.processing.images) percentile_normalize_image() (in module scportrait.tools.spdata.pp) PhenixParser (class in scportrait.tools.parse) plot_he_image() (scportrait.pipeline.project.Project method) plot_input_image() (scportrait.pipeline.project.Project method) plot_qc() (scportrait.tools.stitch.Stitcher method) plot_segmentation_mask() (in module scportrait.plotting) plot_segmentation_masks() (scportrait.pipeline.project.Project method)

precision() (in module scportrait.tools.ml.metrics) print_project_status() (scportrait.pipeline.project.Project method) process() (scportrait.pipeline.extraction.HDF5CellExtraction method) (scportrait.pipeline.featurization.CellFeaturizer method) (scportrait.pipeline.featurization.CellFeaturizer_single_channel method) (scportrait.pipeline.featurization.ConvNeXtFeaturizer method) (scportrait.pipeline.featurization.EnsembleClassifier method) (scportrait.pipeline.featurization.MLClusterClassifier method) (scportrait.pipeline.selection.LMDSelection method) Project (class in scportrait.pipeline.project)

R

RandomRotation (class in scportrait.tools.ml.transforms) read_h5sc() (in module scportrait.io) recall() (in module scportrait.tools.ml.metrics) replace_missing_images() (scportrait.tools.parse.PhenixParser method)

return_id (scportrait.tools.ml.datasets.H5ScSingleCellDataset attribute), [1] (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute), [1] (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute)

S

save_positions() (scportrait.tools.stitch.Stitcher method) scportrait.io module scportrait.pipeline.project module scportrait.pipeline.segmentation.workflows module scportrait.plotting module scportrait.processing.images module scportrait.processing.masks module scportrait.tools.h5sc 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 module scportrait.tools.spdata module

scportrait.tools.spdata.pp module scportrait.tools.stitch module sdata (scportrait.pipeline.project.Project property) sdata_path (scportrait.pipeline.project.Project attribute) select() (scportrait.pipeline.project.Project method) select_channel (scportrait.tools.ml.datasets.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset 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) ShardedWGASegmentation (class in scportrait.pipeline.segmentation.workflows) SizeFilter (class in scportrait.processing.masks) smoothing_kernel_size (scportrait.processing.masks.MatchNucleusCytosolIds attribute) sort_timepoints() (scportrait.tools.parse.PhenixParser method) sort_wells() (scportrait.tools.parse.PhenixParser method) split_dataset_fractions() (in module scportrait.tools.ml.utils) stats() (scportrait.tools.ml.datasets.H5ScSingleCellDataset method) (scportrait.tools.ml.datasets.HDF5SingleCellDataset method) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset method) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset method) stitch() (scportrait.tools.stitch.Stitcher method) Stitcher (class in scportrait.tools.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.H5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.HDF5SingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledH5ScSingleCellDataset attribute) (scportrait.tools.ml.datasets.LabelledHDF5SingleCellDataset attribute)

U

update_cytosol_mask() (scportrait.processing.masks.MatchNucleusCytosolIds method)

update_featurization_f() (scportrait.pipeline.project.Project method) update_masks() (scportrait.processing.masks.MatchNucleusCytosolIds 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) write_image() (in module scportrait.tools.spdata) write_ome_zarr() (scportrait.tools.stitch.Stitcher method)

write_spatialdata() (scportrait.tools.stitch.Stitcher method) write_thumbnail() (scportrait.tools.stitch.Stitcher method) write_tif() (scportrait.tools.stitch.Stitcher method) write_tif_parallel() (scportrait.tools.stitch.ParallelStitcher method)