Index

A

add_layers() (in module cellmap_segmentation_challenge.visualize) alignment (cellmap_segmentation_challenge.utils.crops.CropRow attribute) all_res (cellmap_segmentation_challenge.utils.crops.ZipDatasetRow attribute)

analyze_script() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.security) 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.process module cellmap_segmentation_challenge.cli.speedtest module cellmap_segmentation_challenge.cli.train module cellmap_segmentation_challenge.cli.visualize module cellmap_segmentation_challenge.config 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.predict module cellmap_segmentation_challenge.process module cellmap_segmentation_challenge.train 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.security module cellmap_segmentation_challenge.visualize module CellMapLossWrapper (class in cellmap_segmentation_challenge.utils) (class in cellmap_segmentation_challenge.utils.loss) class_label (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow attribute) CNNEncoder (class in cellmap_segmentation_challenge.models.vitnet) combine_scores() (in module cellmap_segmentation_challenge.evaluate) Config (class in cellmap_segmentation_challenge.utils.security) 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) (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow 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) download_file_with_progress() (in module cellmap_segmentation_challenge.utils.fetch_data)

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_crop_manifest() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.crops) fetch_manifest() (in module cellmap_segmentation_challenge.utils.crops) fetch_test_crop_manifest() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.crops) fetch_zip_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.CellMapLossWrapper method) (cellmap_segmentation_challenge.utils.loss.CellMapLossWrapper method)

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

G

get_3DReg_config() (in module cellmap_segmentation_challenge.models.vitnet) get_chunk_keys() (in module cellmap_segmentation_challenge.utils.fetch_data) get_class_incl_ids() (in module cellmap_segmentation_challenge.utils.datasplit) get_class_relations() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.datasplit) get_csv_string() (in module cellmap_segmentation_challenge.utils.datasplit) get_dataloader() (in module cellmap_segmentation_challenge.utils) (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_formatted_fields() (in module cellmap_segmentation_challenge.utils.datasplit) get_layer() (in module cellmap_segmentation_challenge.visualize) get_raw_path() (in module cellmap_segmentation_challenge.utils.datasplit) get_s3_csv_string() (in module cellmap_segmentation_challenge.utils.datasplit) get_store_url() (in module cellmap_segmentation_challenge.utils.fetch_data) get_test_crops() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.crops) get_tested_classes() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.datasplit) get_zip_if_available() (in module cellmap_segmentation_challenge.utils.fetch_data) gt_source (cellmap_segmentation_challenge.utils.crops.CropRow attribute)

H

hausdorff_distance() (in module cellmap_segmentation_challenge.evaluate)

I

id (cellmap_segmentation_challenge.utils.crops.CropRow attribute) (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow attribute)

L

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

load_safe_config() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.security)

M

make_datasplit_csv() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.datasplit) make_s3_datasplit_csv() (in module cellmap_segmentation_challenge.utils) (in module cellmap_segmentation_challenge.utils.datasplit) match_crop_space() (in module cellmap_segmentation_challenge.evaluate) missing_volume_score() (in module cellmap_segmentation_challenge.evaluate) 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.process cellmap_segmentation_challenge.cli.speedtest cellmap_segmentation_challenge.cli.train cellmap_segmentation_challenge.cli.visualize cellmap_segmentation_challenge.config 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.predict cellmap_segmentation_challenge.process cellmap_segmentation_challenge.train 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.security cellmap_segmentation_challenge.visualize

N

name (cellmap_segmentation_challenge.utils.crops.ZipDatasetRow attribute)

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

package_submission() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.evaluate) padding (cellmap_segmentation_challenge.utils.crops.ZipDatasetRow attribute) parse_s3_url() (in module cellmap_segmentation_challenge.utils.fetch_data) partition_copy_store() (in module cellmap_segmentation_challenge.utils.fetch_data)

predict() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.predict) predict_orthoplanes() (in module cellmap_segmentation_challenge.predict) process() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.process)

R

read_group() (in module cellmap_segmentation_challenge.utils.fetch_data) RegistrationHead (class in cellmap_segmentation_challenge.models.vitnet) resize_array() (in module cellmap_segmentation_challenge.evaluate) 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) (in module cellmap_segmentation_challenge.evaluate) save_numpy_class_labels_to_zarr() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.evaluate) 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) (in module cellmap_segmentation_challenge.evaluate) score_volume() (in module cellmap_segmentation_challenge.evaluate) shape (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow attribute) subset_to_slice() (in module cellmap_segmentation_challenge.utils.fetch_data) swish() (in module cellmap_segmentation_challenge.models.vitnet)

T

TestCropRow (class in cellmap_segmentation_challenge.utils) (class in cellmap_segmentation_challenge.utils.crops) train() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.train)

Transformer (class in cellmap_segmentation_challenge.models.vitnet) translation (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow attribute) 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) url (cellmap_segmentation_challenge.utils.crops.ZipDatasetRow attribute)

V

visualize() (in module cellmap_segmentation_challenge) (in module cellmap_segmentation_challenge.visualize)

ViTVNet (class in cellmap_segmentation_challenge.models.vitnet) voxel_size (cellmap_segmentation_challenge.utils.crops.TestCropRow attribute) (cellmap_segmentation_challenge.utils.TestCropRow attribute)

Z

zip_submission() (in module cellmap_segmentation_challenge.evaluate)

ZipDatasetRow (class in cellmap_segmentation_challenge.utils.crops)