Index

A

alignment (cellmap_segmentation_challenge.utils.crops.CropRow attribute)

Attention (class in cellmap_segmentation_challenge.models.vitnet)

B

Block (class in cellmap_segmentation_challenge.models.vitnet)

build_conv_block() (cellmap_segmentation_challenge.models.resnet.ResnetBlock2D method) (cellmap_segmentation_challenge.models.resnet.ResnetBlock3D method)

C

cellmap_segmentation_challenge module cellmap_segmentation_challenge.cli module cellmap_segmentation_challenge.cli.datasplit module cellmap_segmentation_challenge.cli.evaluate module cellmap_segmentation_challenge.cli.fetch_data module cellmap_segmentation_challenge.cli.predict module cellmap_segmentation_challenge.cli.train module cellmap_segmentation_challenge.evaluate module cellmap_segmentation_challenge.models module cellmap_segmentation_challenge.models.model_load module cellmap_segmentation_challenge.models.resnet module cellmap_segmentation_challenge.models.unet_model_2D module cellmap_segmentation_challenge.models.unet_model_3D module

cellmap_segmentation_challenge.models.vitnet module cellmap_segmentation_challenge.postprocess module cellmap_segmentation_challenge.utils module cellmap_segmentation_challenge.utils.crops module cellmap_segmentation_challenge.utils.dataloader module cellmap_segmentation_challenge.utils.datasplit module cellmap_segmentation_challenge.utils.fetch_data module cellmap_segmentation_challenge.utils.loss module cellmap_segmentation_challenge.utils.visualize module CellMapLossWrapper (class in cellmap_segmentation_challenge.utils.loss) CNNEncoder (class in cellmap_segmentation_challenge.models.vitnet) Conv3dReLU (class in cellmap_segmentation_challenge.models.vitnet) copy_store() (in module cellmap_segmentation_challenge.utils.fetch_data) crop() (cellmap_segmentation_challenge.models.resnet.ResnetBlock2D method) (cellmap_segmentation_challenge.models.resnet.ResnetBlock3D method) CropRow (class in cellmap_segmentation_challenge.utils.crops)

D

dataset (cellmap_segmentation_challenge.utils.crops.CropRow attribute) DecoderBlock (class in cellmap_segmentation_challenge.models.vitnet) DecoderCup (class in cellmap_segmentation_challenge.models.vitnet) DoubleConv (class in cellmap_segmentation_challenge.models.unet_model_2D) (class in cellmap_segmentation_challenge.models.unet_model_3D) (class in cellmap_segmentation_challenge.models.vitnet)

Down (class in cellmap_segmentation_challenge.models.unet_model_2D) (class in cellmap_segmentation_challenge.models.unet_model_3D) (class in cellmap_segmentation_challenge.models.vitnet)

E

em_url (cellmap_segmentation_challenge.utils.crops.CropRow attribute)

Embeddings (class in cellmap_segmentation_challenge.models.vitnet) Encoder (class in cellmap_segmentation_challenge.models.vitnet)

F

fetch_manifest() (in module cellmap_segmentation_challenge.utils.crops) forward() (cellmap_segmentation_challenge.models.resnet.Resnet2D method) (cellmap_segmentation_challenge.models.resnet.Resnet3D method) (cellmap_segmentation_challenge.models.resnet.ResnetBlock2D method) (cellmap_segmentation_challenge.models.resnet.ResnetBlock3D method) (cellmap_segmentation_challenge.models.unet_model_2D.DoubleConv method) (cellmap_segmentation_challenge.models.unet_model_2D.Down method) (cellmap_segmentation_challenge.models.unet_model_2D.OutConv method) (cellmap_segmentation_challenge.models.unet_model_2D.UNet_2D method) (cellmap_segmentation_challenge.models.unet_model_2D.Up method) (cellmap_segmentation_challenge.models.unet_model_3D.DoubleConv method) (cellmap_segmentation_challenge.models.unet_model_3D.Down method) (cellmap_segmentation_challenge.models.unet_model_3D.OutConv method) (cellmap_segmentation_challenge.models.unet_model_3D.UNet_3D method) (cellmap_segmentation_challenge.models.unet_model_3D.Up method) (cellmap_segmentation_challenge.models.vitnet.Attention method) (cellmap_segmentation_challenge.models.vitnet.Block method) (cellmap_segmentation_challenge.models.vitnet.CNNEncoder method) (cellmap_segmentation_challenge.models.vitnet.DecoderBlock method) (cellmap_segmentation_challenge.models.vitnet.DecoderCup method) (cellmap_segmentation_challenge.models.vitnet.DoubleConv method) (cellmap_segmentation_challenge.models.vitnet.Down method) (cellmap_segmentation_challenge.models.vitnet.Embeddings method) (cellmap_segmentation_challenge.models.vitnet.Encoder method) (cellmap_segmentation_challenge.models.vitnet.Mlp method) (cellmap_segmentation_challenge.models.vitnet.Transformer method) (cellmap_segmentation_challenge.models.vitnet.ViTVNet method) (cellmap_segmentation_challenge.utils.loss.CellMapLossWrapper method)

from_csv_row() (cellmap_segmentation_challenge.utils.crops.CropRow class method)

G

get_3DReg_config() (in module cellmap_segmentation_challenge.models.vitnet) get_array_objects() (in module cellmap_segmentation_challenge.utils.fetch_data) get_chunk_keys() (in module cellmap_segmentation_challenge.utils.fetch_data) get_csv_string() (in module cellmap_segmentation_challenge.utils.datasplit) get_dataloader() (in module cellmap_segmentation_challenge.utils.dataloader) get_dataset_counts() (in module cellmap_segmentation_challenge.utils.datasplit)

get_dataset_name() (in module cellmap_segmentation_challenge.utils.datasplit) get_fibsem_path() (in module cellmap_segmentation_challenge.utils.fetch_data) get_group_objects() (in module cellmap_segmentation_challenge.utils.fetch_data) get_raw_path() (in module cellmap_segmentation_challenge.utils.datasplit) get_store_url() (in module cellmap_segmentation_challenge.utils.fetch_data) get_url() (in module cellmap_segmentation_challenge.utils.fetch_data) gt_url (cellmap_segmentation_challenge.utils.crops.CropRow attribute)

I

id (cellmap_segmentation_challenge.utils.crops.CropRow attribute)

L

load_best_val() (in module cellmap_segmentation_challenge.models.model_load)

load_latest() (in module cellmap_segmentation_challenge.models.model_load)

M

make_datasplit_csv() (in module cellmap_segmentation_challenge.utils.datasplit) Mlp (class in cellmap_segmentation_challenge.models.vitnet) module cellmap_segmentation_challenge cellmap_segmentation_challenge.cli cellmap_segmentation_challenge.cli.datasplit cellmap_segmentation_challenge.cli.evaluate cellmap_segmentation_challenge.cli.fetch_data cellmap_segmentation_challenge.cli.predict cellmap_segmentation_challenge.cli.train cellmap_segmentation_challenge.evaluate cellmap_segmentation_challenge.models cellmap_segmentation_challenge.models.model_load cellmap_segmentation_challenge.models.resnet cellmap_segmentation_challenge.models.unet_model_2D cellmap_segmentation_challenge.models.unet_model_3D cellmap_segmentation_challenge.models.vitnet cellmap_segmentation_challenge.postprocess cellmap_segmentation_challenge.utils cellmap_segmentation_challenge.utils.crops cellmap_segmentation_challenge.utils.dataloader cellmap_segmentation_challenge.utils.datasplit cellmap_segmentation_challenge.utils.fetch_data cellmap_segmentation_challenge.utils.loss cellmap_segmentation_challenge.utils.visualize

N

np2th() (in module cellmap_segmentation_challenge.models.vitnet)

O

OutConv (class in cellmap_segmentation_challenge.models.unet_model_2D) (class in cellmap_segmentation_challenge.models.unet_model_3D)

P

partition_copy_store() (in module cellmap_segmentation_challenge.utils.fetch_data)

predict() (in module cellmap_segmentation_challenge) process_volume() (in module cellmap_segmentation_challenge.postprocess)

R

read_group() (in module cellmap_segmentation_challenge.utils.fetch_data) RegistrationHead (class in cellmap_segmentation_challenge.models.vitnet) rescale_volume() (in module cellmap_segmentation_challenge.postprocess) resize_volume() (in module cellmap_segmentation_challenge.postprocess) ResNet (class in cellmap_segmentation_challenge.models.resnet)

Resnet2D (class in cellmap_segmentation_challenge.models.resnet) Resnet3D (class in cellmap_segmentation_challenge.models.resnet) ResnetBlock2D (class in cellmap_segmentation_challenge.models.resnet) ResnetBlock3D (class in cellmap_segmentation_challenge.models.resnet) resolve_em_url() (in module cellmap_segmentation_challenge.utils.fetch_data)

S

save_numpy_class_arrays_to_zarr() (in module cellmap_segmentation_challenge.evaluate) save_numpy_class_labels_to_zarr() (in module cellmap_segmentation_challenge.evaluate) save_result_figs() (in module cellmap_segmentation_challenge.utils.visualize) score_instance() (in module cellmap_segmentation_challenge.evaluate) score_label() (in module cellmap_segmentation_challenge.evaluate)

score_semantic() (in module cellmap_segmentation_challenge.evaluate) score_submission() (in module cellmap_segmentation_challenge.evaluate) score_volume() (in module cellmap_segmentation_challenge.evaluate) subset_to_slice() (in module cellmap_segmentation_challenge.utils.fetch_data) swish() (in module cellmap_segmentation_challenge.models.vitnet)

T

threshold_volume() (in module cellmap_segmentation_challenge.postprocess) train() (in module cellmap_segmentation_challenge)

Transformer (class in cellmap_segmentation_challenge.models.vitnet) transpose_for_scores() (cellmap_segmentation_challenge.models.vitnet.Attention method)

U

UNet_2D (class in cellmap_segmentation_challenge.models.unet_model_2D) UNet_3D (class in cellmap_segmentation_challenge.models.unet_model_3D)

unzip_file() (in module cellmap_segmentation_challenge.evaluate) Up (class in cellmap_segmentation_challenge.models.unet_model_2D) (class in cellmap_segmentation_challenge.models.unet_model_3D)

V

ViTVNet (class in cellmap_segmentation_challenge.models.vitnet)