Index

A

ActThreshLabel (class in cyto_dl.models.im2im.utils.postprocessing.act_thresh_label) add_mask_tokens() (cyto_dl.nn.vits.decoder.MAE_Decoder method) AddMeta (class in cyto_dl.image.transforms.add_meta) adjust_indices_for_cls() (cyto_dl.nn.vits.decoder.MAE_Decoder method) AdversarialLoss (class in cyto_dl.nn.losses.adversarial_loss) after_save_checkpoint() (cyto_dl.loggers.mlflow.MLFlowLogger method)

AICSImageLoaderd (class in cyto_dl.image.io.aicsimage_loader) AlternatingBatchSampler (class in cyto_dl.datamodules.dataframe.utils) append_class_weights() (in module cyto_dl.dataframe.transforms.misc) append_labels_to_integers() (in module cyto_dl.dataframe.transforms.misc) append_one_hot() (in module cyto_dl.dataframe.transforms.misc) AutoThreshold (class in cyto_dl.models.im2im.utils.postprocessing.auto_thresh) AutoThresholdMethod (class in cyto_dl.api.data)

B

BaseHead (class in cyto_dl.nn.head.base_head) BaseModel (class in cyto_dl.models.base_model) BaseModelMeta (class in cyto_dl.models.base_model) BaseVAE (class in cyto_dl.models.vae.base_vae)

BasicModel (class in cyto_dl.models.basic_model) batch_pairwise_dist() (cyto_dl.nn.losses.chamfer_loss.ChamferLoss method) batch_pairwise_dist2() (cyto_dl.nn.losses.chamfer_loss.ChamferLoss method) BrightSampler (class in cyto_dl.image.transforms.bright_sampler)

C

calculate_elbo() (cyto_dl.models.vae.base_vae.BaseVAE method) calculate_mahalanobis_hook() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) calculate_rcl() (cyto_dl.models.vae.base_vae.BaseVAE method) calculate_rcl_dict() (cyto_dl.models.vae.base_vae.BaseVAE method) Caltech101 (class in cyto_dl.datamodules.torchvision) Caltech256 (class in cyto_dl.datamodules.torchvision) CBLogLoss (class in cyto_dl.nn.losses.continuous_bernoulli) CelebA (class in cyto_dl.datamodules.torchvision) centroid_to_slice() (cyto_dl.image.transforms.crop_to_seg.CentroidCrop method) CentroidCrop (class in cyto_dl.image.transforms.crop_to_seg) CentroidCropd (class in cyto_dl.image.transforms.crop_to_seg) ChamferLoss (class in cyto_dl.nn.losses.chamfer_loss) CIFAR10 (class in cyto_dl.datamodules.torchvision) CIFAR100 (class in cyto_dl.datamodules.torchvision) Cityscapes (class in cyto_dl.datamodules.torchvision) Classification (class in cyto_dl.models.classification.classification) CLEVRClassification (class in cyto_dl.datamodules.torchvision) Clip (class in cyto_dl.image.transforms.clip) Clipd (class in cyto_dl.image.transforms.clip) close_loggers() (in module cyto_dl.utils.template_utils) cluster_object() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegCluster method) CMAP_loss (class in cyto_dl.nn.losses.loss_wrapper) CocoCaptions (class in cyto_dl.datamodules.torchvision) CocoDetection (class in cyto_dl.datamodules.torchvision) compute_metrics() (cyto_dl.models.base_model.BaseModel method) compute_rotation_matrix() (cyto_dl.utils.rotation.RotationModule method) compute_tc_penalty() (in module cyto_dl.models.vae.priors.gaussian) configure_optimizers() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.im2im.gan.GAN method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) (cyto_dl.models.jepa.jepa_base.JEPABase method) ContrastAdjust (class in cyto_dl.image.transforms.contrastadjust) ContrastAdjustd (class in cyto_dl.image.transforms.contrastadjust) Contrastive (class in cyto_dl.models.contrastive.contrastive) ConvPoolReLU (class in cyto_dl.nn.spatial_transformer) CosineLoss (class in cyto_dl.nn.losses.cosine_loss) Country211 (class in cyto_dl.datamodules.torchvision) CPU (cyto_dl.api.data.HardwareType attribute) create_conv() (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) create_dataloader() (in module cyto_dl.utils.array) create_img2token() (cyto_dl.nn.vits.blocks.patchify.patchify.Patchify method) (cyto_dl.nn.vits.blocks.patchify.patchify_hiera.PatchifyHiera method) create_metatensor() (cyto_dl.datamodules.multidim_image.MultiDimImageDataset method) create_patch2img() (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) CropResize (class in cyto_dl.image.transforms.track_transforms) CrossAttention (class in cyto_dl.nn.vits.blocks.cross_attention) CrossAttentionBlock (class in cyto_dl.nn.vits.blocks.cross_attention) CrossMAE_Decoder (class in cyto_dl.nn.vits.decoder) CrossSelfBlock (class in cyto_dl.nn.vits.blocks.cross_attention) CSVSaver (class in cyto_dl.callbacks.csv_saver) cyto_dl module cyto_dl.api module cyto_dl.api.cyto_dl_model module cyto_dl.api.cyto_dl_model.cyto_dl_base_model module cyto_dl.api.cyto_dl_model.segmentation_plugin_model module cyto_dl.api.data module cyto_dl.api.model module cyto_dl.callbacks module cyto_dl.callbacks.csv_saver module cyto_dl.callbacks.image_saver module cyto_dl.callbacks.layer_freeze module cyto_dl.callbacks.model_utils module cyto_dl.callbacks.outlier_detection module cyto_dl.dataframe module cyto_dl.dataframe.readers module cyto_dl.dataframe.transforms module cyto_dl.dataframe.transforms.filter module cyto_dl.dataframe.transforms.group_cols module cyto_dl.dataframe.transforms.misc module cyto_dl.dataframe.transforms.split module cyto_dl.datamodules module cyto_dl.datamodules.array module cyto_dl.datamodules.data_dict module cyto_dl.datamodules.dataframe module cyto_dl.datamodules.dataframe.dataframe_datamodule module cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule module cyto_dl.datamodules.dataframe.utils module cyto_dl.datamodules.folder module cyto_dl.datamodules.multidim_image module cyto_dl.datamodules.smartcache module cyto_dl.datamodules.torchvision module cyto_dl.eval module cyto_dl.image module cyto_dl.image.io module cyto_dl.image.io.aicsimage_loader module cyto_dl.image.io.monai_bio_reader module cyto_dl.image.io.numpy_reader module cyto_dl.image.io.ome_zarr_reader module cyto_dl.image.io.polygon_loader module cyto_dl.image.io.skimage_reader module cyto_dl.image.transforms module cyto_dl.image.transforms.add_meta module cyto_dl.image.transforms.bright_sampler module cyto_dl.image.transforms.clip module cyto_dl.image.transforms.contrastadjust module cyto_dl.image.transforms.crop_to_seg module cyto_dl.image.transforms.generate_jepa_masks module cyto_dl.image.transforms.merge module cyto_dl.image.transforms.multiscale_cropper module cyto_dl.image.transforms.pad module cyto_dl.image.transforms.project module cyto_dl.image.transforms.save module cyto_dl.image.transforms.track_transforms module cyto_dl.loggers module cyto_dl.loggers.mlflow module cyto_dl.models module cyto_dl.models.base_model module cyto_dl.models.basic_model module cyto_dl.models.classification module

cyto_dl.models.classification.classification module cyto_dl.models.classification.timepoint_classification module cyto_dl.models.contrastive module cyto_dl.models.contrastive.contrastive module cyto_dl.models.im2im module cyto_dl.models.im2im.gan module cyto_dl.models.im2im.multi_task module cyto_dl.models.im2im.utils module cyto_dl.models.im2im.utils.instance_seg module cyto_dl.models.im2im.utils.noise_annealer module cyto_dl.models.im2im.utils.postprocessing module cyto_dl.models.im2im.utils.postprocessing.act_thresh_label module cyto_dl.models.im2im.utils.postprocessing.auto_thresh module cyto_dl.models.im2im.utils.postprocessing.dict_to_im module cyto_dl.models.jepa module cyto_dl.models.jepa.ijepa module cyto_dl.models.jepa.iwm module cyto_dl.models.jepa.jepa_base module cyto_dl.models.utils module cyto_dl.models.utils.mlflow module cyto_dl.models.utils.utils module cyto_dl.models.vae.base_vae module cyto_dl.models.vae.priors module cyto_dl.models.vae.priors.abstract_prior module cyto_dl.models.vae.priors.gaussian module cyto_dl.models.vae.priors.identity_prior module cyto_dl.models.vae.priors.joint_prior module cyto_dl.nn module cyto_dl.nn.discriminators module cyto_dl.nn.discriminators.multi_scale_discriminator module cyto_dl.nn.discriminators.n_layer_discriminator module cyto_dl.nn.head module cyto_dl.nn.head.base_head module cyto_dl.nn.head.gan_head module cyto_dl.nn.head.gan_head_superres module cyto_dl.nn.head.mae_head module cyto_dl.nn.head.mask_head module cyto_dl.nn.head.res_blocks_head module cyto_dl.nn.head.vic_reg module cyto_dl.nn.hr_skip module cyto_dl.nn.losses module cyto_dl.nn.losses.adversarial_loss module cyto_dl.nn.losses.chamfer_loss module cyto_dl.nn.losses.continuous_bernoulli module cyto_dl.nn.losses.cosine_loss module cyto_dl.nn.losses.gan_loss module cyto_dl.nn.losses.gaussian_nll_loss module cyto_dl.nn.losses.loss_wrapper module cyto_dl.nn.losses.threshold_loss module cyto_dl.nn.losses.vic_reg module cyto_dl.nn.losses.weibull module cyto_dl.nn.losses.weighted_mse_loss module cyto_dl.nn.mlp module cyto_dl.nn.res_unit module cyto_dl.nn.spatial_transformer module cyto_dl.nn.track_sequence_predictor module cyto_dl.nn.vits module cyto_dl.nn.vits.blocks module cyto_dl.nn.vits.blocks.cross_attention module cyto_dl.nn.vits.blocks.intermediate_weigher module cyto_dl.nn.vits.blocks.masked_unit_attention module cyto_dl.nn.vits.blocks.patchify module cyto_dl.nn.vits.blocks.patchify.patchify module cyto_dl.nn.vits.blocks.patchify.patchify_base module cyto_dl.nn.vits.blocks.patchify.patchify_hiera module cyto_dl.nn.vits.decoder module cyto_dl.nn.vits.encoder module cyto_dl.nn.vits.mae module cyto_dl.nn.vits.predictor module cyto_dl.nn.vits.seg module cyto_dl.nn.vits.utils module cyto_dl.point_cloud module cyto_dl.train module cyto_dl.utils module cyto_dl.utils.array module cyto_dl.utils.checkpoint module cyto_dl.utils.config module cyto_dl.utils.download_test_data module cyto_dl.utils.dummy_dataset module cyto_dl.utils.pylogger module cyto_dl.utils.rich_utils module cyto_dl.utils.rotation module cyto_dl.utils.template_utils module CytoDLBaseModel (class in cyto_dl.api.cyto_dl_model.cyto_dl_base_model) CytoDLModel (class in cyto_dl.api.model)

D

DataframeDatamodule (class in cyto_dl.datamodules.dataframe.dataframe_datamodule) DatasetFolder (class in cyto_dl.datamodules.torchvision) decode() (cyto_dl.models.vae.base_vae.BaseVAE method) decoder (cyto_dl.nn.vits.mae.HieraMAE property) (cyto_dl.nn.vits.mae.MAE property) (cyto_dl.nn.vits.mae.MAE_Base property) delete_test_data() (in module cyto_dl.utils.download_test_data)

detach() (in module cyto_dl.models.im2im.utils.postprocessing.dict_to_im) DiagonalGaussianPrior (class in cyto_dl.models.vae.priors.gaussian) DictToIm (class in cyto_dl.models.im2im.utils.postprocessing.dict_to_im) download_example_data() (cyto_dl.api.model.CytoDLModel method) download_test_data() (in module cyto_dl.utils.download_test_data) DTD (class in cyto_dl.datamodules.torchvision) DummyDatamodule (class in cyto_dl.utils.dummy_dataset) DummyDataset (class in cyto_dl.utils.dummy_dataset)

E

embed_from_skel() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) EMNIST (class in cyto_dl.datamodules.torchvision) encode() (cyto_dl.models.vae.base_vae.BaseVAE method) EncodedSkip (class in cyto_dl.nn.vits.seg) encoder (cyto_dl.nn.vits.mae.HieraMAE property) (cyto_dl.nn.vits.mae.MAE property) (cyto_dl.nn.vits.mae.MAE_Base property) enforce_tags() (in module cyto_dl.utils.rich_utils)

EuroSAT (class in cyto_dl.datamodules.torchvision) ExperimentType (class in cyto_dl.api.data) extract_array_predictions() (in module cyto_dl.utils.array) extract_embeddings() (cyto_dl.models.jepa.iwm.IWM method) extract_visible_tokens() (cyto_dl.nn.vits.blocks.patchify.patchify.Patchify method) (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) (cyto_dl.nn.vits.blocks.patchify.patchify_hiera.PatchifyHiera method) extras() (in module cyto_dl.utils.template_utils)

F

FakeData (class in cyto_dl.datamodules.torchvision) FashionMNIST (class in cyto_dl.datamodules.torchvision) FER2013 (class in cyto_dl.datamodules.torchvision) FGVCAircraft (class in cyto_dl.datamodules.torchvision) filter_columns() (in module cyto_dl.dataframe.readers) (in module cyto_dl.dataframe.transforms.filter) filter_rows() (in module cyto_dl.dataframe.transforms.filter) find_indices() (in module cyto_dl.models.utils.utils) flatten_activations() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) Flickr30k (class in cyto_dl.datamodules.torchvision) Flickr8k (class in cyto_dl.datamodules.torchvision) Flowers102 (class in cyto_dl.datamodules.torchvision) Food101 (class in cyto_dl.datamodules.torchvision) forward() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.basic_model.BasicModel method) (cyto_dl.models.classification.classification.Classification method) (cyto_dl.models.contrastive.contrastive.Contrastive method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) (cyto_dl.models.jepa.jepa_base.JEPABase method) (cyto_dl.models.vae.base_vae.BaseVAE method) (cyto_dl.models.vae.priors.abstract_prior.Prior method) (cyto_dl.models.vae.priors.gaussian.DiagonalGaussianPrior method) (cyto_dl.models.vae.priors.gaussian.IsotropicGaussianPrior method) (cyto_dl.models.vae.priors.identity_prior.IdentityPrior method) (cyto_dl.models.vae.priors.joint_prior.JointPrior method) (cyto_dl.nn.discriminators.multi_scale_discriminator.MultiScaleDiscriminator method) (cyto_dl.nn.discriminators.n_layer_discriminator.NLayerDiscriminator method) (cyto_dl.nn.head.base_head.BaseHead method) (cyto_dl.nn.head.gan_head.GANHead method) (cyto_dl.nn.head.gan_head_superres.GANHead_resize method) (cyto_dl.nn.head.res_blocks_head.ResBlocksHead method) (cyto_dl.nn.hr_skip.HRSkip method) (cyto_dl.nn.losses.adversarial_loss.AdversarialLoss method) (cyto_dl.nn.losses.chamfer_loss.ChamferLoss method) (cyto_dl.nn.losses.continuous_bernoulli.CBLogLoss method) (cyto_dl.nn.losses.cosine_loss.CosineLoss method) (cyto_dl.nn.losses.gaussian_nll_loss.GaussianNLLLoss method) (cyto_dl.nn.losses.vic_reg.VICRegLoss method) (cyto_dl.nn.losses.weibull.WeibullLogLoss method) (cyto_dl.nn.losses.weighted_mse_loss.WeightedMSELoss method) (cyto_dl.nn.mlp.MLP method) (cyto_dl.nn.res_unit.ResidualUnit method) (cyto_dl.nn.spatial_transformer.ConvPoolReLU method) (cyto_dl.nn.spatial_transformer.STN method) (cyto_dl.nn.track_sequence_predictor.TrackClassifier method) (cyto_dl.nn.vits.blocks.cross_attention.CrossAttention method) (cyto_dl.nn.vits.blocks.cross_attention.CrossAttentionBlock method) (cyto_dl.nn.vits.blocks.cross_attention.CrossSelfBlock method) (cyto_dl.nn.vits.blocks.cross_attention.Mlp method) (cyto_dl.nn.vits.blocks.intermediate_weigher.IntermediateWeigher method) (cyto_dl.nn.vits.blocks.masked_unit_attention.HieraBlock method) (cyto_dl.nn.vits.blocks.masked_unit_attention.MaskUnitAttention method) (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) (cyto_dl.nn.vits.decoder.CrossMAE_Decoder method) (cyto_dl.nn.vits.decoder.MAE_Decoder method) (cyto_dl.nn.vits.encoder.HieraEncoder method) (cyto_dl.nn.vits.encoder.JEPAEncoder method) (cyto_dl.nn.vits.encoder.MAE_Encoder method) (cyto_dl.nn.vits.encoder.SpatialMerger method) (cyto_dl.nn.vits.mae.MAE_Base method) (cyto_dl.nn.vits.predictor.IWMPredictor method) (cyto_dl.nn.vits.predictor.JEPAPredictor method) (cyto_dl.nn.vits.seg.EncodedSkip method) (cyto_dl.nn.vits.seg.Seg_ViT method) (cyto_dl.nn.vits.seg.SuperresDecoder method)

from_default_config() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel class method) from_existing_config() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel class method)

G

GAN (class in cyto_dl.models.im2im.gan) (cyto_dl.api.data.ExperimentType attribute) GANHead (class in cyto_dl.nn.head.gan_head) GANHead_resize (class in cyto_dl.nn.head.gan_head_superres) GANLoss (class in cyto_dl.nn.losses.gan_loss) GaussianNLLLoss (class in cyto_dl.nn.losses.gaussian_nll_loss) generate_img() (cyto_dl.utils.dummy_dataset.DummyDataset method) generate_io_map() (cyto_dl.nn.head.base_head.BaseHead method) generate_slices() (cyto_dl.image.transforms.multiscale_cropper.RandomMultiScaleCropd method) GenerateTrackLabels (class in cyto_dl.image.transforms.track_transforms) get_all_embeddings() (in module cyto_dl.callbacks.model_utils) get_canonical_split_name() (in module cyto_dl.datamodules.dataframe.utils) get_centroids() (cyto_dl.image.transforms.crop_to_seg.SegCropd method) get_config() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method) (in module cyto_dl.models.utils.mlflow) get_context_embeddings() (cyto_dl.models.jepa.jepa_base.JEPABase method) get_data() (cyto_dl.image.io.monai_bio_reader.MonaiBioReader method) (cyto_dl.image.io.ome_zarr_reader.OmeZarrReader method) (cyto_dl.image.io.skimage_reader.SkimageReader method) get_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.utils.dummy_dataset.DummyDatamodule method) get_dataset() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (in module cyto_dl.datamodules.dataframe.utils) get_experiment_name() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method) get_feature_matching_loss() (cyto_dl.nn.losses.gan_loss.Pix2PixHD method) get_gan_loss() (cyto_dl.nn.losses.gan_loss.Pix2PixHD method) get_hardware_type() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method)

get_input_channel() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) get_manifest_column_names() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) get_mask() (cyto_dl.models.jepa.jepa_base.JEPABase method) (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) get_mask_args() (cyto_dl.nn.vits.blocks.patchify.patchify.Patchify method) (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase method) (cyto_dl.nn.vits.blocks.patchify.patchify_hiera.PatchifyHiera method) get_metric_value() (in module cyto_dl.utils.template_utils) get_n_postprocess_image() (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) get_patch_size() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) get_per_file_args() (cyto_dl.datamodules.multidim_image.MultiDimImageDataset method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) get_per_head() (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) get_positional_embedding() (in module cyto_dl.nn.vits.utils) get_predict_masks() (cyto_dl.models.jepa.iwm.IWM method) get_pylogger() (in module cyto_dl.utils.pylogger) get_raw_image_channels() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) get_rotation_matrix_so2() (in module cyto_dl.utils.rotation) get_rotation_matrix_so3() (in module cyto_dl.utils.rotation) get_split_column() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) get_target_embeddings() (cyto_dl.models.jepa.jepa_base.JEPABase method) get_target_tensor() (cyto_dl.nn.losses.gan_loss.GANLoss method) GetEmbeddings (class in cyto_dl.callbacks.model_utils) GPU (cyto_dl.api.data.HardwareType attribute) GroupCols (class in cyto_dl.dataframe.transforms.group_cols) GroupedDataframeDatamodule (class in cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule) GTSRB (class in cyto_dl.datamodules.torchvision)

H

HardwareType (class in cyto_dl.api.data) HieraBlock (class in cyto_dl.nn.vits.blocks.masked_unit_attention) HieraEncoder (class in cyto_dl.nn.vits.encoder)

HieraMAE (class in cyto_dl.nn.vits.mae) HMDB51 (class in cyto_dl.datamodules.torchvision) HRSkip (class in cyto_dl.nn.hr_skip)

I

IdentityPrior (class in cyto_dl.models.vae.priors.identity_prior) IJEPA (class in cyto_dl.models.jepa.ijepa) ImageFolder (class in cyto_dl.datamodules.torchvision) ImageNet (class in cyto_dl.datamodules.torchvision) ImageSaver (class in cyto_dl.callbacks.image_saver) img2token (cyto_dl.nn.vits.blocks.patchify.patchify.Patchify property) (cyto_dl.nn.vits.blocks.patchify.patchify_base.PatchifyBase property) (cyto_dl.nn.vits.blocks.patchify.patchify_hiera.PatchifyHiera property) INaturalist (class in cyto_dl.datamodules.torchvision) init_decoder() (cyto_dl.nn.vits.mae.MAE_Base method) init_encoder() (cyto_dl.nn.vits.mae.MAE_Base method) init_weight() (cyto_dl.nn.vits.decoder.MAE_Decoder method) (cyto_dl.nn.vits.encoder.MAE_Encoder method) (cyto_dl.nn.vits.predictor.JEPAPredictor method)

INSTANCE_SEG (cyto_dl.api.data.ExperimentType attribute) InstanceSegCluster (class in cyto_dl.models.im2im.utils.instance_seg) InstanceSegLoss (class in cyto_dl.models.im2im.utils.instance_seg) InstanceSegPreprocessd (class in cyto_dl.models.im2im.utils.instance_seg) InstanceSegRandFlipd (class in cyto_dl.models.im2im.utils.instance_seg) instantiate_callbacks() (in module cyto_dl.utils.template_utils) instantiate_loggers() (in module cyto_dl.utils.template_utils) IntermediateWeigher (class in cyto_dl.nn.vits.blocks.intermediate_weigher) is_batch() (cyto_dl.datamodules.multidim_image.MultiDimImageDataset method) is_config() (in module cyto_dl.utils.config) ISODATA (cyto_dl.api.data.AutoThresholdMethod attribute) IsotropicGaussianPrior (class in cyto_dl.models.vae.priors.gaussian) IWM (class in cyto_dl.models.jepa.iwm) IWMPredictor (class in cyto_dl.nn.vits.predictor)

J

JEPABase (class in cyto_dl.models.jepa.jepa_base) JEPAEncoder (class in cyto_dl.nn.vits.encoder) JEPAMaskGenerator (class in cyto_dl.image.transforms.generate_jepa_masks)

JEPAPredictor (class in cyto_dl.nn.vits.predictor) JEPASaver (class in cyto_dl.callbacks.csv_saver) JointPrior (class in cyto_dl.models.vae.priors.joint_prior)

K

kd_clustering() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegCluster method) keep_largest_cc() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) Kinetics (class in cyto_dl.datamodules.torchvision) Kitti (class in cyto_dl.datamodules.torchvision) kl_divergence() (cyto_dl.models.vae.priors.abstract_prior.Prior method) (cyto_dl.models.vae.priors.gaussian.DiagonalGaussianPrior class method) (cyto_dl.models.vae.priors.gaussian.IsotropicGaussianPrior class method) (cyto_dl.models.vae.priors.joint_prior.JointPrior method)

KMNIST (class in cyto_dl.datamodules.torchvision) kv_to_dict() (in module cyto_dl.utils.config)

L

label_2d() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) LABEL_FREE (cyto_dl.api.data.ExperimentType attribute) LARGE (cyto_dl.api.data.PatchSize attribute) LayerFreeze (class in cyto_dl.callbacks.layer_freeze) LFWPairs (class in cyto_dl.datamodules.torchvision) LFWPeople (class in cyto_dl.datamodules.torchvision) LI (cyto_dl.api.data.AutoThresholdMethod attribute) load_checkpoint() (in module cyto_dl.utils.checkpoint) load_config_from_dict() (cyto_dl.api.model.CytoDLModel method)

load_config_from_file() (cyto_dl.api.model.CytoDLModel method) load_default_experiment() (cyto_dl.api.model.CytoDLModel method) load_model_from_checkpoint() (in module cyto_dl.models.utils.mlflow) LOCAL (cyto_dl.api.data.AutoThresholdMethod attribute) log_hyperparameters() (in module cyto_dl.utils.template_utils) log_hyperparams() (cyto_dl.loggers.mlflow.MLFlowLogger method) log_metrics() (cyto_dl.loggers.mlflow.MLFlowLogger method) LossWrapper (class in cyto_dl.nn.losses.loss_wrapper) LSUN (class in cyto_dl.datamodules.torchvision) LSUNClass (class in cyto_dl.datamodules.torchvision)

M

MAE (class in cyto_dl.nn.vits.mae) MAE_Base (class in cyto_dl.nn.vits.mae) MAE_Decoder (class in cyto_dl.nn.vits.decoder) MAE_Encoder (class in cyto_dl.nn.vits.encoder) MAEHead (class in cyto_dl.nn.head.mae_head) main() (in module cyto_dl.eval) (in module cyto_dl.train) make_array_dataloader() (in module cyto_dl.datamodules.array) make_data_dict_dataloader() (in module cyto_dl.datamodules.data_dict) make_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule.GroupedDataframeDatamodule method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) make_folder_dataloader() (in module cyto_dl.datamodules.folder) make_multidim_image_dataloader() (in module cyto_dl.datamodules.multidim_image) make_multiple_dataframe_splits() (in module cyto_dl.datamodules.dataframe.utils) make_random_df() (in module cyto_dl.dataframe.transforms.misc) make_single_dataframe_splits() (in module cyto_dl.datamodules.dataframe.utils) MaskHead (class in cyto_dl.nn.head.mask_head) MaskUnitAttention (class in cyto_dl.nn.vits.blocks.masked_unit_attention) match_tuple_dimensions() (in module cyto_dl.nn.vits.utils) MaxProjectd (class in cyto_dl.image.transforms.project) MEAN (cyto_dl.api.data.AutoThresholdMethod attribute) MEDIUM (cyto_dl.api.data.PatchSize attribute) Merged (class in cyto_dl.image.transforms.merge) MINIMUM (cyto_dl.api.data.AutoThresholdMethod attribute) MLFlowLogger (class in cyto_dl.loggers.mlflow) MLP (class in cyto_dl.nn.mlp) Mlp (class in cyto_dl.nn.vits.blocks.cross_attention) MNIST (class in cyto_dl.datamodules.torchvision) model_step() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.basic_model.BasicModel method) (cyto_dl.models.classification.classification.Classification method) (cyto_dl.models.contrastive.contrastive.Contrastive method) (cyto_dl.models.im2im.gan.GAN method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) (cyto_dl.models.jepa.ijepa.IJEPA method) (cyto_dl.models.jepa.iwm.IWM method) (cyto_dl.models.jepa.jepa_base.JEPABase method) (cyto_dl.models.vae.base_vae.BaseVAE method) module cyto_dl cyto_dl.api cyto_dl.api.cyto_dl_model cyto_dl.api.cyto_dl_model.cyto_dl_base_model cyto_dl.api.cyto_dl_model.segmentation_plugin_model cyto_dl.api.data cyto_dl.api.model cyto_dl.callbacks cyto_dl.callbacks.csv_saver cyto_dl.callbacks.image_saver cyto_dl.callbacks.layer_freeze cyto_dl.callbacks.model_utils cyto_dl.callbacks.outlier_detection cyto_dl.dataframe cyto_dl.dataframe.readers cyto_dl.dataframe.transforms cyto_dl.dataframe.transforms.filter cyto_dl.dataframe.transforms.group_cols cyto_dl.dataframe.transforms.misc cyto_dl.dataframe.transforms.split cyto_dl.datamodules cyto_dl.datamodules.array cyto_dl.datamodules.data_dict cyto_dl.datamodules.dataframe cyto_dl.datamodules.dataframe.dataframe_datamodule cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule cyto_dl.datamodules.dataframe.utils cyto_dl.datamodules.folder cyto_dl.datamodules.multidim_image cyto_dl.datamodules.smartcache cyto_dl.datamodules.torchvision cyto_dl.eval cyto_dl.image cyto_dl.image.io cyto_dl.image.io.aicsimage_loader cyto_dl.image.io.monai_bio_reader cyto_dl.image.io.numpy_reader cyto_dl.image.io.ome_zarr_reader cyto_dl.image.io.polygon_loader cyto_dl.image.io.skimage_reader cyto_dl.image.transforms cyto_dl.image.transforms.add_meta cyto_dl.image.transforms.bright_sampler cyto_dl.image.transforms.clip cyto_dl.image.transforms.contrastadjust cyto_dl.image.transforms.crop_to_seg cyto_dl.image.transforms.generate_jepa_masks cyto_dl.image.transforms.merge cyto_dl.image.transforms.multiscale_cropper cyto_dl.image.transforms.pad cyto_dl.image.transforms.project cyto_dl.image.transforms.save cyto_dl.image.transforms.track_transforms cyto_dl.loggers cyto_dl.loggers.mlflow cyto_dl.models cyto_dl.models.base_model cyto_dl.models.basic_model cyto_dl.models.classification cyto_dl.models.classification.classification cyto_dl.models.classification.timepoint_classification cyto_dl.models.contrastive cyto_dl.models.contrastive.contrastive cyto_dl.models.im2im cyto_dl.models.im2im.gan cyto_dl.models.im2im.multi_task cyto_dl.models.im2im.utils cyto_dl.models.im2im.utils.instance_seg cyto_dl.models.im2im.utils.noise_annealer cyto_dl.models.im2im.utils.postprocessing cyto_dl.models.im2im.utils.postprocessing.act_thresh_label cyto_dl.models.im2im.utils.postprocessing.auto_thresh cyto_dl.models.im2im.utils.postprocessing.dict_to_im cyto_dl.models.jepa cyto_dl.models.jepa.ijepa cyto_dl.models.jepa.iwm cyto_dl.models.jepa.jepa_base cyto_dl.models.utils cyto_dl.models.utils.mlflow cyto_dl.models.utils.utils cyto_dl.models.vae.base_vae cyto_dl.models.vae.priors cyto_dl.models.vae.priors.abstract_prior cyto_dl.models.vae.priors.gaussian cyto_dl.models.vae.priors.identity_prior cyto_dl.models.vae.priors.joint_prior cyto_dl.nn cyto_dl.nn.discriminators cyto_dl.nn.discriminators.multi_scale_discriminator cyto_dl.nn.discriminators.n_layer_discriminator cyto_dl.nn.head cyto_dl.nn.head.base_head cyto_dl.nn.head.gan_head cyto_dl.nn.head.gan_head_superres cyto_dl.nn.head.mae_head cyto_dl.nn.head.mask_head cyto_dl.nn.head.res_blocks_head cyto_dl.nn.head.vic_reg cyto_dl.nn.hr_skip cyto_dl.nn.losses cyto_dl.nn.losses.adversarial_loss cyto_dl.nn.losses.chamfer_loss cyto_dl.nn.losses.continuous_bernoulli cyto_dl.nn.losses.cosine_loss cyto_dl.nn.losses.gan_loss cyto_dl.nn.losses.gaussian_nll_loss cyto_dl.nn.losses.loss_wrapper cyto_dl.nn.losses.threshold_loss cyto_dl.nn.losses.vic_reg cyto_dl.nn.losses.weibull cyto_dl.nn.losses.weighted_mse_loss cyto_dl.nn.mlp cyto_dl.nn.res_unit cyto_dl.nn.spatial_transformer cyto_dl.nn.track_sequence_predictor cyto_dl.nn.vits cyto_dl.nn.vits.blocks cyto_dl.nn.vits.blocks.cross_attention cyto_dl.nn.vits.blocks.intermediate_weigher cyto_dl.nn.vits.blocks.masked_unit_attention cyto_dl.nn.vits.blocks.patchify cyto_dl.nn.vits.blocks.patchify.patchify cyto_dl.nn.vits.blocks.patchify.patchify_base cyto_dl.nn.vits.blocks.patchify.patchify_hiera cyto_dl.nn.vits.decoder cyto_dl.nn.vits.encoder cyto_dl.nn.vits.mae cyto_dl.nn.vits.predictor cyto_dl.nn.vits.seg cyto_dl.nn.vits.utils cyto_dl.point_cloud cyto_dl.train cyto_dl.utils cyto_dl.utils.array cyto_dl.utils.checkpoint cyto_dl.utils.config cyto_dl.utils.download_test_data cyto_dl.utils.dummy_dataset cyto_dl.utils.pylogger cyto_dl.utils.rich_utils cyto_dl.utils.rotation cyto_dl.utils.template_utils

MonaiBioReader (class in cyto_dl.image.io.monai_bio_reader) MovingMNIST (class in cyto_dl.datamodules.torchvision) MultiDimImageDataset (class in cyto_dl.datamodules.multidim_image) MULTIOTSU (cyto_dl.api.data.AutoThresholdMethod attribute) MultiScaleDiscriminator (class in cyto_dl.nn.discriminators.multi_scale_discriminator) MultiTaskIm2Im (class in cyto_dl.models.im2im.multi_task)

N

NIBLACK (cyto_dl.api.data.AutoThresholdMethod attribute)

NLayerDiscriminator (class in cyto_dl.nn.discriminators.n_layer_discriminator) NoiseAnnealer (class in cyto_dl.models.im2im.utils.noise_annealer)

O

off_diagonal() (in module cyto_dl.nn.losses.vic_reg) OmeZarrReader (class in cyto_dl.image.io.ome_zarr_reader) Omniglot (class in cyto_dl.datamodules.torchvision) on_load_checkpoint() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_predict_batch_end() (cyto_dl.callbacks.image_saver.ImageSaver method) (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_predict_epoch_end() (cyto_dl.callbacks.csv_saver.CSVSaver method) on_predict_epoch_start() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_save_checkpoint() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_test_batch_end() (cyto_dl.callbacks.image_saver.ImageSaver method) (cyto_dl.callbacks.outlier_detection.OutlierDetection method)

on_test_epoch_end() (cyto_dl.callbacks.model_utils.GetEmbeddings method) on_test_epoch_start() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_train_batch_end() (cyto_dl.callbacks.image_saver.ImageSaver method) on_train_epoch_start() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) on_train_start() (cyto_dl.models.base_model.BaseModel method) on_validation_batch_end() (cyto_dl.callbacks.image_saver.ImageSaver method) OTSU (cyto_dl.api.data.AutoThresholdMethod attribute) OutlierDetection (class in cyto_dl.callbacks.outlier_detection) override_config() (cyto_dl.api.model.CytoDLModel method) OxfordIIITPet (class in cyto_dl.datamodules.torchvision)

P

pad_slice() (in module cyto_dl.models.im2im.utils.instance_seg) PadZd (class in cyto_dl.image.transforms.pad) param_size (cyto_dl.models.vae.priors.abstract_prior.Prior property) (cyto_dl.models.vae.priors.gaussian.DiagonalGaussianPrior property) (cyto_dl.models.vae.priors.gaussian.IsotropicGaussianPrior property) (cyto_dl.models.vae.priors.identity_prior.IdentityPrior property) (cyto_dl.models.vae.priors.joint_prior.JointPrior property) parse_batch() (cyto_dl.models.base_model.BaseModel method) parse_s3_path() (in module cyto_dl.utils.download_test_data) parse_transforms() (in module cyto_dl.datamodules.dataframe.utils) Patchify (class in cyto_dl.nn.vits.blocks.patchify.patchify) PatchifyBase (class in cyto_dl.nn.vits.blocks.patchify.patchify_base) PatchifyHiera (class in cyto_dl.nn.vits.blocks.patchify.patchify_hiera) PatchSize (class in cyto_dl.api.data) PCAM (class in cyto_dl.datamodules.torchvision) PerChannel (class in cyto_dl.image.transforms.track_transforms) PhotoTour (class in cyto_dl.datamodules.torchvision) Pix2PixHD (class in cyto_dl.nn.losses.gan_loss) Places365 (class in cyto_dl.datamodules.torchvision) plot_classes() (cyto_dl.models.contrastive.contrastive.Contrastive method) plot_neighbors() (cyto_dl.models.contrastive.contrastive.Contrastive method)

PolygonLoaderd (class in cyto_dl.image.io.polygon_loader) positionalencoding1d() (in module cyto_dl.nn.track_sequence_predictor) pred_to_csv() (cyto_dl.callbacks.csv_saver.CSVSaver method) (cyto_dl.callbacks.csv_saver.JEPASaver method) predict() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method) (cyto_dl.api.model.CytoDLModel method) predict_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) (cyto_dl.utils.dummy_dataset.DummyDatamodule method) predict_step() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.classification.classification.Classification method) (cyto_dl.models.classification.timepoint_classification.TimepointClassification method) (cyto_dl.models.contrastive.contrastive.Contrastive method) (cyto_dl.models.im2im.gan.GAN method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) (cyto_dl.models.jepa.iwm.IWM method) (cyto_dl.models.jepa.jepa_base.JEPABase method) predict_target_features() (cyto_dl.nn.vits.predictor.JEPAPredictor method) prepare_data() (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) print_config() (cyto_dl.api.model.CytoDLModel method) print_config_tree() (in module cyto_dl.utils.rich_utils) Prior (class in cyto_dl.models.vae.priors.abstract_prior)

Q

QMNIST (class in cyto_dl.datamodules.torchvision)

R

random_indexes() (in module cyto_dl.nn.vits.utils) RandomMultiScaleCropd (class in cyto_dl.image.transforms.multiscale_cropper) read() (cyto_dl.image.io.monai_bio_reader.MonaiBioReader method) (cyto_dl.image.io.ome_zarr_reader.OmeZarrReader method) (cyto_dl.image.io.skimage_reader.SkimageReader method) read_csv() (in module cyto_dl.dataframe.readers) read_dataframe() (in module cyto_dl.dataframe.readers) read_h5ad() (in module cyto_dl.dataframe.readers) read_parquet() (in module cyto_dl.dataframe.readers) ReadNumpyFile (class in cyto_dl.image.io.numpy_reader) remove_aux_key() (in module cyto_dl.utils.config) remove_excess_pixels() (cyto_dl.image.transforms.generate_jepa_masks.JEPAMaskGenerator method) remove_first_dim() (cyto_dl.models.jepa.jepa_base.JEPABase method)

remove_small_skeletons() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegCluster method) remove_split_column() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) RemoveNaNKeysd (class in cyto_dl.datamodules.dataframe.utils) RenderedSST2 (class in cyto_dl.datamodules.torchvision) ResBlocksHead (class in cyto_dl.nn.head.res_blocks_head) ResidualUnit (class in cyto_dl.nn.res_unit) RotationModule (class in cyto_dl.utils.rotation) run_forward() (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) run_head() (cyto_dl.nn.head.base_head.BaseHead method) (cyto_dl.nn.head.gan_head.GANHead method) (cyto_dl.nn.head.mae_head.MAEHead method) (cyto_dl.nn.head.mask_head.MaskHead method) (cyto_dl.nn.head.vic_reg.VICRegHead method)

S

sample() (cyto_dl.models.vae.priors.abstract_prior.Prior method) (cyto_dl.models.vae.priors.gaussian.IsotropicGaussianPrior class method) (cyto_dl.models.vae.priors.joint_prior.JointPrior method) sample_n_each() (in module cyto_dl.dataframe.transforms.split) sample_z() (cyto_dl.models.vae.base_vae.BaseVAE method) SAUVOLA (cyto_dl.api.data.AutoThresholdMethod attribute) Save (class in cyto_dl.image.transforms.save) save() (cyto_dl.callbacks.image_saver.ImageSaver method) save_config() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method) (cyto_dl.api.model.CytoDLModel method) save_feats() (cyto_dl.callbacks.csv_saver.CSVSaver method) save_file() (in module cyto_dl.utils.template_utils) save_images() (cyto_dl.models.classification.classification.Classification method) save_predictions_classifier() (in module cyto_dl.callbacks.model_utils) Saved (class in cyto_dl.image.transforms.save) SBDataset (class in cyto_dl.datamodules.torchvision) SBU (class in cyto_dl.datamodules.torchvision) Seg_ViT (class in cyto_dl.nn.vits.seg) SegCropd (class in cyto_dl.image.transforms.crop_to_seg) SEGMENTATION (cyto_dl.api.data.ExperimentType attribute) SEGMENTATION_ARRAY (cyto_dl.api.data.ExperimentType attribute) SEGMENTATION_PLUGIN (cyto_dl.api.data.ExperimentType attribute) SegmentationPluginModel (class in cyto_dl.api.cyto_dl_model.segmentation_plugin_model) SEMEION (class in cyto_dl.datamodules.torchvision) set_experiment_name() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method)

set_hardware_type() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) set_input_channel() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) set_manifest_column_names() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) set_patch_size() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) set_raw_image_channels() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) set_split_column() (cyto_dl.api.cyto_dl_model.segmentation_plugin_model.SegmentationPluginModel method) setup() (cyto_dl.callbacks.layer_freeze.LayerFreeze method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) setup_paths() (in module cyto_dl.utils.download_test_data) should_save_image() (cyto_dl.models.classification.classification.Classification method) shrink() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) skeleton_tall() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) SkimageReader (class in cyto_dl.image.io.skimage_reader) SMALL (cyto_dl.api.data.PatchSize attribute) SmartcacheDatamodule (class in cyto_dl.datamodules.smartcache) smooth_embedding() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) SpatialMerger (class in cyto_dl.nn.vits.encoder) split_args() (cyto_dl.image.io.aicsimage_loader.AICSImageLoaderd method) split_dataframe() (in module cyto_dl.dataframe.transforms.split) SplitTrackd (class in cyto_dl.image.transforms.track_transforms) StanfordCars (class in cyto_dl.datamodules.torchvision) STL10 (class in cyto_dl.datamodules.torchvision) STN (class in cyto_dl.nn.spatial_transformer) SUN397 (class in cyto_dl.datamodules.torchvision) SuperresDecoder (class in cyto_dl.nn.vits.seg) SVHN (class in cyto_dl.datamodules.torchvision)

T

take_indexes() (in module cyto_dl.nn.vits.utils) take_indexes_mask() (in module cyto_dl.nn.vits.blocks.patchify.patchify_hiera) task_wrapper() (in module cyto_dl.utils.template_utils) test_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) (cyto_dl.utils.dummy_dataset.DummyDatamodule method) test_step() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) (cyto_dl.models.jepa.iwm.IWM method) ThresholdLoss (class in cyto_dl.nn.losses.threshold_loss) TimepointClassification (class in cyto_dl.models.classification.timepoint_classification)

toggle() (cyto_dl.nn.spatial_transformer.STN method) topology_preserving_thinning() (cyto_dl.models.im2im.utils.instance_seg.InstanceSegPreprocessd method) TrackClassifier (class in cyto_dl.nn.track_sequence_predictor) train() (cyto_dl.api.cyto_dl_model.cyto_dl_base_model.CytoDLBaseModel method) (cyto_dl.api.model.CytoDLModel method) train_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) (cyto_dl.utils.dummy_dataset.DummyDatamodule method) training_step() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) TRIANGLE (cyto_dl.api.data.AutoThresholdMethod attribute)

U

UCF101 (class in cyto_dl.datamodules.torchvision) update_covariance_hook() (cyto_dl.callbacks.outlier_detection.OutlierDetection method) update_noise() (cyto_dl.models.im2im.utils.noise_annealer.NoiseAnnealer method)

update_params() (cyto_dl.nn.head.base_head.BaseHead method) update_teacher() (cyto_dl.models.jepa.jepa_base.JEPABase method) USPS (class in cyto_dl.datamodules.torchvision)

V

val_dataloader() (cyto_dl.datamodules.dataframe.dataframe_datamodule.DataframeDatamodule method) (cyto_dl.datamodules.smartcache.SmartcacheDatamodule method) (cyto_dl.utils.dummy_dataset.DummyDatamodule method) validation_step() (cyto_dl.models.base_model.BaseModel method) (cyto_dl.models.im2im.multi_task.MultiTaskIm2Im method) verify_suffix() (cyto_dl.image.io.monai_bio_reader.MonaiBioReader method) (cyto_dl.image.io.ome_zarr_reader.OmeZarrReader method) (cyto_dl.image.io.skimage_reader.SkimageReader method)

VICRegHead (class in cyto_dl.nn.head.vic_reg) VICRegLoss (class in cyto_dl.nn.losses.vic_reg) VisionDataset (class in cyto_dl.datamodules.torchvision) VOCDetection (class in cyto_dl.datamodules.torchvision) VOCSegmentation (class in cyto_dl.datamodules.torchvision)

W

weibull_log_probs() (in module cyto_dl.nn.losses.weibull) WeibullLogLoss (class in cyto_dl.nn.losses.weibull)

WeightedMSELoss (class in cyto_dl.nn.losses.weighted_mse_loss) WIDERFace (class in cyto_dl.datamodules.torchvision)

Y

YEN (cyto_dl.api.data.AutoThresholdMethod attribute)