Index

C

calculate_normalization() (in module nimbus_inference.utils) cell_id_select_fn() (nimbus_inference.cell_analyzer.CellAnalyzer method) CellAnalyzer (class in nimbus_inference.cell_analyzer) check_inputs() (nimbus_inference.nimbus.Nimbus method) (nimbus_inference.utils.MultiplexDataset method)

ConvBlock (class in nimbus_inference.unet) create_composite_from_dataset() (nimbus_inference.viewer_widget.NimbusViewer method) create_composite_image() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method) create_instance_image() (nimbus_inference.cell_analyzer.CellAnalyzer method) CropConcatBlock (class in nimbus_inference.unet)

D

display() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method)

F

filter_channels() (nimbus_inference.utils.MultiplexDataset method) forward() (nimbus_inference.unet.ConvBlock method) (nimbus_inference.unet.CropConcatBlock method) (nimbus_inference.unet.Pad2D method) (nimbus_inference.unet.UNet method) (nimbus_inference.unet.UpconvBlock method)

G

get_channel() (nimbus_inference.utils.LazyOMETIFFReader method) (nimbus_inference.utils.MultiplexDataset method) get_channel_names() (nimbus_inference.utils.LazyOMETIFFReader method) get_channel_single() (nimbus_inference.utils.MultiplexDataset method) get_channel_stack() (nimbus_inference.utils.MultiplexDataset method)

get_channels() (nimbus_inference.utils.MultiplexDataset method) get_fovs() (nimbus_inference.utils.MultiplexDataset method) get_metadata() (nimbus_inference.utils.LazyOMETIFFReader method) get_segmentation() (nimbus_inference.utils.MultiplexDataset method) get_shape() (nimbus_inference.utils.LazyOMETIFFReader method)

H

HidePrints (class in nimbus_inference.utils)

I

initialize_model() (nimbus_inference.nimbus.Nimbus method)

is_multi_channel_tiff() (nimbus_inference.utils.MultiplexDataset method)

L

layout() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method)

LazyOMETIFFReader (class in nimbus_inference.utils)

M

maybe_crop() (in module nimbus_inference.unet) module nimbus_inference nimbus_inference.cell_analyzer nimbus_inference.nimbus nimbus_inference.unet nimbus_inference.utils nimbus_inference.viewer_widget

MultiplexDataset (class in nimbus_inference.utils)

N

Nimbus (class in nimbus_inference.nimbus) nimbus_inference module nimbus_inference.cell_analyzer module nimbus_inference.nimbus module nimbus_inference.unet module

nimbus_inference.utils module nimbus_inference.viewer_widget module nimbus_preprocess() (in module nimbus_inference.nimbus) (in module nimbus_inference.utils) NimbusViewer (class in nimbus_inference.viewer_widget)

O

overlay() (nimbus_inference.viewer_widget.NimbusViewer method)

P

Pad2D (class in nimbus_inference.unet) predict_fovs() (in module nimbus_inference.utils) (nimbus_inference.nimbus.Nimbus method) predict_segmentation() (nimbus_inference.nimbus.Nimbus method)

prep_naming_convention() (in module nimbus_inference.nimbus) prepare_input_data() (in module nimbus_inference.utils) prepare_normalization_dict() (in module nimbus_inference.utils) (nimbus_inference.nimbus.Nimbus method)

S

save_annotations_button_click() (nimbus_inference.cell_analyzer.CellAnalyzer method) search_for_similar() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method)

segment_mean() (in module nimbus_inference.utils) select_fov() (nimbus_inference.viewer_widget.NimbusViewer method)

T

test_time_aug() (in module nimbus_inference.utils)

U

UNet (class in nimbus_inference.unet) UpconvBlock (class in nimbus_inference.unet) update_button_click() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method)

update_composite() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method) update_img() (nimbus_inference.cell_analyzer.CellAnalyzer method) (nimbus_inference.viewer_widget.NimbusViewer method)