Index

_

__getitem__() (cellmap_data.CellMapDataLoader method) (cellmap_data.CellMapDataset method) (cellmap_data.CellMapImage method) (cellmap_data.dataloader.CellMapDataLoader method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) (cellmap_data.image.CellMapImage method) (cellmap_data.image.EmptyImage method)

__init__() (cellmap_data.CellMapDataLoader method) (cellmap_data.CellMapDataset method) (cellmap_data.CellMapDataSplit method) (cellmap_data.CellMapImage method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.CellMapSubset method) __len__() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method)

A

add_multiscale_metadata_levels() (in module cellmap_data.utils.metadata) align_coords() (cellmap_data.image.ImageWriter method) aligned_coords_from_center() (cellmap_data.image.ImageWriter method) apply_spatial_transforms() (cellmap_data.CellMapImage method) (cellmap_data.image.CellMapImage method)

array (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.ImageWriter property) array_path (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property)

B

bg_count (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.EmptyImage property) blocks (cellmap_data.dataset_writer.CellMapDatasetWriter property) bounding_box (cellmap_data.CellMapDataset property) (cellmap_data.CellMapImage property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.EmptyImage property)

bounding_box_shape (cellmap_data.CellMapDataset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property)

C

cellmap_data module cellmap_data.dataloader module cellmap_data.dataset module cellmap_data.dataset_writer module cellmap_data.datasplit module cellmap_data.image module cellmap_data.multidataset module cellmap_data.subdataset module cellmap_data.transforms module cellmap_data.transforms.augment module cellmap_data.transforms.augment.gaussian_noise module cellmap_data.transforms.augment.nan_to_num module cellmap_data.transforms.augment.normalize module cellmap_data.transforms.augment.random_contrast module cellmap_data.transforms.augment.random_gamma module cellmap_data.transforms.targets module cellmap_data.transforms.targets.cellpose module cellmap_data.transforms.targets.distance module cellmap_data.utils module cellmap_data.utils.dtype module cellmap_data.utils.figs module cellmap_data.utils.metadata module CellMapDataLoader (class in cellmap_data) (class in cellmap_data.dataloader) CellMapDataset (class in cellmap_data) (class in cellmap_data.dataset)

CellMapDatasetWriter (class in cellmap_data.dataset_writer) CellMapDataSplit (class in cellmap_data) (class in cellmap_data.datasplit) CellMapImage (class in cellmap_data) (class in cellmap_data.image) CellMapMultiDataset (class in cellmap_data) (class in cellmap_data.multidataset) CellMapSubset (class in cellmap_data) (class in cellmap_data.subdataset) CellposeFlow (class in cellmap_data.transforms.targets.cellpose) center (cellmap_data.CellMapDataset property) (cellmap_data.CellMapImage property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.ImageWriter property) chunk_shape (cellmap_data.image.ImageWriter property) class_counts (cellmap_data.CellMapDataset property) (cellmap_data.CellMapDataSplit property) (cellmap_data.CellMapImage property) (cellmap_data.CellMapMultiDataset property) (cellmap_data.CellMapSubset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.datasplit.CellMapDataSplit property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.EmptyImage property) (cellmap_data.multidataset.CellMapMultiDataset property) (cellmap_data.subdataset.CellMapSubset property) class_weights (cellmap_data.CellMapDataset property) (cellmap_data.CellMapMultiDataset property) (cellmap_data.CellMapSubset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.multidataset.CellMapMultiDataset property) (cellmap_data.subdataset.CellMapSubset property) classes (cellmap_data.CellMapMultiDataset attribute) (cellmap_data.CellMapSubset property) (cellmap_data.multidataset.CellMapMultiDataset attribute) (cellmap_data.subdataset.CellMapSubset property) collate_fn() (cellmap_data.CellMapDataLoader method) (cellmap_data.dataloader.CellMapDataLoader method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) construct() (cellmap_data.CellMapDataSplit method) (cellmap_data.datasplit.CellMapDataSplit method) coordinateTransformations (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) create_multiscale_metadata() (in module cellmap_data.utils.metadata) cumulative_sizes (cellmap_data.multidataset.CellMapMultiDataset attribute)

D

dataset (cellmap_data.subdataset.CellMapSubset attribute) dataset_weights (cellmap_data.CellMapMultiDataset property) (cellmap_data.multidataset.CellMapMultiDataset property) datasets (cellmap_data.CellMapMultiDataset attribute) (cellmap_data.multidataset.CellMapMultiDataset attribute), [1]

device (cellmap_data.CellMapDataset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) DistanceTransform (class in cellmap_data.transforms.targets.distance)

E

empty() (cellmap_data.CellMapDataset static method) (cellmap_data.CellMapMultiDataset static method) (cellmap_data.dataset.CellMapDataset static method) (cellmap_data.multidataset.CellMapMultiDataset static method)

EmptyImage (class in cellmap_data.image)

F

find_level() (cellmap_data.CellMapImage method) (cellmap_data.image.CellMapImage method) forward() (cellmap_data.transforms.augment.gaussian_noise.GaussianNoise method) (cellmap_data.transforms.augment.random_contrast.RandomContrast method) (cellmap_data.transforms.augment.random_gamma.RandomGamma method) (cellmap_data.transforms.targets.distance.DistanceTransform method) (cellmap_data.transforms.targets.distance.SignedDistanceTransform method)

from_csv() (cellmap_data.CellMapDataSplit method) (cellmap_data.datasplit.CellMapDataSplit method) full_coords (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.ImageWriter property)

G

GaussianNoise (class in cellmap_data.transforms.augment.gaussian_noise) generate_base_multiscales_metadata() (in module cellmap_data.utils.metadata) generate_spatial_transforms() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) get_center() (cellmap_data.dataset_writer.CellMapDatasetWriter method) get_empty_store() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) get_image_dict() (in module cellmap_data.utils.figs) get_image_grid() (in module cellmap_data.utils.figs) get_image_grid_numpy() (in module cellmap_data.utils.figs) get_image_writer() (cellmap_data.dataset_writer.CellMapDatasetWriter method) get_indices() (cellmap_data.CellMapDataset method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) (cellmap_data.multidataset.CellMapMultiDataset method)

get_label_array() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) get_subset_random_sampler() (cellmap_data.CellMapMultiDataset method) (cellmap_data.multidataset.CellMapMultiDataset method) get_target_array() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) get_target_array_writer() (cellmap_data.dataset_writer.CellMapDatasetWriter method) get_weighted_sampler() (cellmap_data.CellMapMultiDataset method) (cellmap_data.multidataset.CellMapMultiDataset method) group (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property)

I

ImageWriter (class in cellmap_data.image) indices (cellmap_data.subdataset.CellMapSubset attribute)

input_arrays (cellmap_data.CellMapMultiDataset attribute) (cellmap_data.multidataset.CellMapMultiDataset attribute)

L

largest_voxel_sizes (cellmap_data.CellMapDataset property) (cellmap_data.dataset.CellMapDataset property)

loader() (cellmap_data.dataset_writer.CellMapDatasetWriter method)

M

module cellmap_data cellmap_data.dataloader cellmap_data.dataset cellmap_data.dataset_writer cellmap_data.datasplit cellmap_data.image cellmap_data.multidataset cellmap_data.subdataset cellmap_data.transforms cellmap_data.transforms.augment cellmap_data.transforms.augment.gaussian_noise cellmap_data.transforms.augment.nan_to_num cellmap_data.transforms.augment.normalize cellmap_data.transforms.augment.random_contrast cellmap_data.transforms.augment.random_gamma cellmap_data.transforms.targets cellmap_data.transforms.targets.cellpose cellmap_data.transforms.targets.distance cellmap_data.utils cellmap_data.utils.dtype cellmap_data.utils.figs cellmap_data.utils.metadata

multiscale_attrs (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property)

N

NaNtoNum (class in cellmap_data.transforms.augment.nan_to_num)

Normalize (class in cellmap_data.transforms.augment.normalize)

O

offset (cellmap_data.image.ImageWriter property)

R

RandomContrast (class in cellmap_data.transforms.augment.random_contrast) RandomGamma (class in cellmap_data.transforms.augment.random_gamma) refresh() (cellmap_data.CellMapDataLoader method) (cellmap_data.dataloader.CellMapDataLoader method) reset_arrays() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method)

return_data() (cellmap_data.CellMapImage method) (cellmap_data.image.CellMapImage method) rotate_coords() (cellmap_data.CellMapImage method) (cellmap_data.image.CellMapImage method)

S

sample_weights (cellmap_data.CellMapMultiDataset property) (cellmap_data.multidataset.CellMapMultiDataset property) sampling_box (cellmap_data.CellMapDataset property) (cellmap_data.CellMapImage property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.EmptyImage property) sampling_box_shape (cellmap_data.CellMapDataset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) scale_level (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) set_arrays() (cellmap_data.CellMapDataSplit method) (cellmap_data.datasplit.CellMapDataSplit method) set_raw_value_transforms() (cellmap_data.CellMapDataset method) (cellmap_data.CellMapDataSplit method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.CellMapSubset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) (cellmap_data.datasplit.CellMapDataSplit method) (cellmap_data.multidataset.CellMapMultiDataset method) (cellmap_data.subdataset.CellMapSubset method) set_spatial_transforms() (cellmap_data.CellMapDataSplit method) (cellmap_data.CellMapImage method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.datasplit.CellMapDataSplit method) (cellmap_data.image.CellMapImage method) (cellmap_data.image.EmptyImage method) (cellmap_data.multidataset.CellMapMultiDataset method)

set_target_value_transforms() (cellmap_data.CellMapDataset method) (cellmap_data.CellMapDataSplit method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.CellMapSubset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.datasplit.CellMapDataSplit method) (cellmap_data.multidataset.CellMapMultiDataset method) (cellmap_data.subdataset.CellMapSubset method) shape (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property) (cellmap_data.image.ImageWriter property) SignedDistanceTransform (class in cellmap_data.transforms.targets.distance) size (cellmap_data.CellMapDataset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.dataset_writer.CellMapDatasetWriter property) smallest_target_array (cellmap_data.dataset_writer.CellMapDatasetWriter property) smallest_voxel_sizes (cellmap_data.dataset_writer.CellMapDatasetWriter property) split_target_path() (in module cellmap_data.dataset) (in module cellmap_data.dataset_writer)

T

target_arrays (cellmap_data.CellMapMultiDataset attribute) (cellmap_data.multidataset.CellMapMultiDataset attribute) to() (cellmap_data.CellMapDataset method) (cellmap_data.CellMapImage method) (cellmap_data.CellMapMultiDataset method) (cellmap_data.CellMapSubset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) (cellmap_data.image.CellMapImage method) (cellmap_data.image.EmptyImage method) (cellmap_data.multidataset.CellMapMultiDataset method) (cellmap_data.subdataset.CellMapSubset method)

torch_max_value() (in module cellmap_data.utils.dtype) train_datasets_combined (cellmap_data.CellMapDataSplit property) (cellmap_data.datasplit.CellMapDataSplit property) transform() (in module cellmap_data.transforms.targets.distance) translation (cellmap_data.CellMapImage property) (cellmap_data.image.CellMapImage property)

V

validation_blocks (cellmap_data.CellMapDataSplit property) (cellmap_data.datasplit.CellMapDataSplit property) validation_datasets_combined (cellmap_data.CellMapDataSplit property) (cellmap_data.datasplit.CellMapDataSplit property) validation_indices (cellmap_data.CellMapDataset property) (cellmap_data.CellMapMultiDataset property) (cellmap_data.CellMapSubset property) (cellmap_data.dataset.CellMapDataset property) (cellmap_data.multidataset.CellMapMultiDataset property) (cellmap_data.subdataset.CellMapSubset property)

verify() (cellmap_data.CellMapDataset method) (cellmap_data.dataset.CellMapDataset method) (cellmap_data.dataset_writer.CellMapDatasetWriter method) verify_datasets() (cellmap_data.CellMapDataSplit method) (cellmap_data.datasplit.CellMapDataSplit method)

W

world_shape (cellmap_data.image.ImageWriter property)

write_metadata() (in module cellmap_data.utils.metadata) writer_indices (cellmap_data.dataset_writer.CellMapDatasetWriter property)