Index _ | A | B | C | D | E | F | G | H | K | L | M | N | O | P | R | S | T | U | V | W | X | Y _ __getitem__() (piscis.data.MultiSpotsDataset method) (piscis.data.SpotsDataset method) __iter__() (piscis.data.SpotsDataStream method) (piscis.data.WeightedDatasetSampler method) __len__() (piscis.data.MultiSpotsDataset method) (piscis.data.SpotsDataset method) (piscis.data.SpotsDataStream method) (piscis.data.WeightedDatasetSampler method) _apply() (piscis.core._Piscis method) _compute_metrics() (in module piscis.metrics) _gaussian() (in module piscis.utils) _get_worker_info() (piscis.data.SpotsDataStream static method) _make_sampler() (piscis.data.SpotsDataStream method) _match_coords() (in module piscis.utils) _Piscis (class in piscis.core) _postprocess_stack() (piscis.core._Piscis static method) _predict() (piscis.core._Piscis method) _predict_plane() (piscis.core._Piscis method) _predict_stack() (piscis.core._Piscis method) _preprocess() (piscis.core._Piscis method) _process() (piscis.core._Piscis method) A act (piscis.networks.conv.SqueezeExcite attribute) adjust() (in module piscis.transforms) adjust_parameters() (in module piscis.core) adjustment (piscis.data.SpotsDataset attribute) apply() (piscis.transforms.RandomAugment method) augment (piscis.transforms.RandomAugment attribute) augment_cls (piscis.data.SpotsDataStream attribute) B batch_adjust() (in module piscis.transforms) batch_size (piscis.core._Piscis attribute) batch_voronoi_transform() (in module piscis.transforms) BatchActConv (in module piscis.networks.fpn) BatchConv (in module piscis.networks.fpn) BatchConvStyle (class in piscis.networks.fpn) block (piscis.networks.conv.FusedMBConv attribute) (piscis.networks.conv.MBConv attribute) BLOCK_ARGS (in module piscis.models.spots) blocks (piscis.networks.efficientnetv2.EfficientNetV2 attribute) build_efficientnetv2() (in module piscis.networks.efficientnetv2) C cached_indices (piscis.data.SpotsDataStream attribute) CHECKPOINTS_DIR (in module piscis.paths) compute_metrics() (in module piscis.metrics) compute_spot_coordinates() (in module piscis.utils) Conv (class in piscis.networks.conv) conv (piscis.networks.conv.Conv attribute) (piscis.networks.fpn.BatchConvStyle attribute) (piscis.networks.fpn.UpConv attribute) Conv2d (class in piscis.models.spots) ConvBatchAct (in module piscis.networks.conv) convert_dataset() (in module piscis.convert) convert_jax_to_torch_state_dict() (in module piscis.convert) convs_0 (piscis.networks.fpn.UpConv attribute) convs_1 (piscis.networks.fpn.UpConv attribute) convs_2 (piscis.networks.fpn.UpConv attribute) D dataset (piscis.data.SpotsDataStream attribute) datasets (piscis.data.MultiSpotsDataset attribute) (piscis.data.WeightedDatasetSampler attribute) Decoder (class in piscis.networks.fpn) decoder (piscis.networks.fpn.FPN attribute) DEFAULT_BLOCKS_ARGS (in module piscis.networks.efficientnetv2_defaults) deformable_max_pool() (in module piscis.utils) deformable_softmax_pool() (in module piscis.utils) deformable_sum_pool() (in module piscis.utils) dense (piscis.networks.fpn.BatchConvStyle attribute) device (piscis.core._Piscis attribute) download_dataset() (in module piscis.downloads) download_pretrained_model() (in module piscis.downloads) E EfficientNetV2 (class in piscis.networks.efficientnetv2) EfficientNetV2B0 (in module piscis.networks.efficientnetv2) EfficientNetV2B1 (in module piscis.networks.efficientnetv2) EfficientNetV2B2 (in module piscis.networks.efficientnetv2) EfficientNetV2B3 (in module piscis.networks.efficientnetv2) EfficientNetV2L (in module piscis.networks.efficientnetv2) EfficientNetV2M (in module piscis.networks.efficientnetv2) EfficientNetV2S (in module piscis.networks.efficientnetv2) encoder (piscis.networks.fpn.FPN attribute) encoder_levels (piscis.networks.fpn.FPN attribute) epoch (piscis.data.SpotsDataStream attribute) epoch_size (piscis.data.MultiSpotsDataset attribute) expand (piscis.networks.conv.SqueezeExcite attribute) F fit_coords() (in module piscis.utils) forward() (piscis.models.spots.SpotsModel method) (piscis.networks.conv.Conv method) (piscis.networks.conv.FusedMBConv method) (piscis.networks.conv.MBConv method) (piscis.networks.conv.SqueezeExcite method) (piscis.networks.efficientnetv2.EfficientNetV2 method) (piscis.networks.fpn.BatchConvStyle method) (piscis.networks.fpn.Decoder method) (piscis.networks.fpn.FPN method) (piscis.networks.fpn.MakeStyle method) (piscis.networks.fpn.UpConv method) FPN (class in piscis.networks.fpn) fpn (piscis.models.spots.SpotsModel attribute) FusedMBConv (class in piscis.networks.conv) G generate_dataset() (in module piscis.data) generator (piscis.data.WeightedDatasetSampler attribute) get_torch_dataloader() (in module piscis.data) get_torch_dataset() (in module piscis.data) H HF_DATASETS_DIR (in module piscis.paths) HF_MODELS_DIR (in module piscis.paths) K kernel_size (piscis.models.spots.SpotsModel attribute) L Linear (class in piscis.models.spots) linear_sum_assignment() (in module piscis.metrics) list_datasets() (in module piscis.downloads) list_pretrained_models() (in module piscis.downloads) load_dataset() (in module piscis.data) load_datasets() (in module piscis.data) loss_fn() (in module piscis.training) M main() (in module piscis.__main__) MakeStyle (class in piscis.networks.fpn) masked_l2_loss() (in module piscis.losses) MBConv (class in piscis.networks.conv) mean_masked_l2_loss (in module piscis.losses) mean_smoothf1_loss (in module piscis.losses) min_num_samples (piscis.data.SpotsDataStream attribute) model (piscis.core._Piscis attribute) model_name (piscis.core._Piscis attribute) MODELS_DIR (in module piscis.paths) module piscis piscis.__main__ piscis.convert piscis.core piscis.data piscis.downloads piscis.losses piscis.metrics piscis.models piscis.models.spots piscis.networks piscis.networks.conv piscis.networks.efficientnetv2 piscis.networks.efficientnetv2_defaults piscis.networks.fpn piscis.paths piscis.training piscis.transforms piscis.utils ModuleDef (in module piscis.networks.conv) (in module piscis.networks.efficientnetv2) (in module piscis.networks.fpn) MultiSpotsDataset (class in piscis.data) N next_epoch() (piscis.data.SpotsDataStream method) normalize() (in module piscis.transforms) O out_channels (piscis.networks.fpn.Decoder attribute) output (piscis.networks.fpn.FPN attribute) output_size (piscis.transforms.RandomAugment attribute) P pad() (in module piscis.utils) pad_and_stack() (in module piscis.utils) peak_local_softmax() (in module piscis.utils) piscis module Piscis (class in piscis) (class in piscis.core) piscis.__main__ module piscis.convert module piscis.core module piscis.data module piscis.downloads module piscis.losses module piscis.metrics module piscis.models module piscis.models.spots module piscis.networks module piscis.networks.conv module piscis.networks.efficientnetv2 module piscis.networks.efficientnetv2_defaults module piscis.networks.fpn module piscis.paths module piscis.training module piscis.transforms module piscis.utils module PISCIS_DIR (in module piscis.paths) PiscisLegacy (class in piscis) (class in piscis.core) pooling (piscis.core._Piscis attribute) predict() (piscis.core.Piscis method) (piscis.core.PiscisLegacy method) (piscis.Piscis method) (piscis.PiscisLegacy method) proj (piscis.networks.fpn.UpConv attribute) R RandomAugment (class in piscis.transforms) reduce (piscis.networks.conv.SqueezeExcite attribute) reduce_loss() (in module piscis.losses) remove_duplicate_coords() (in module piscis.utils) reset_parameters() (piscis.models.spots.Conv2d method) (piscis.models.spots.Linear method) resize_up_blocks (piscis.networks.fpn.Decoder attribute) rng (piscis.transforms.RandomAugment attribute) round_features() (in module piscis.networks.efficientnetv2) round_input_size() (in module piscis.models.spots) round_repeats() (in module piscis.networks.efficientnetv2) S seed (piscis.data.SpotsDataStream attribute) (piscis.data.WeightedDatasetSampler attribute) set_epoch() (piscis.data.SpotsDataStream method) shuffle (piscis.data.SpotsDataStream attribute) sigmoid (piscis.models.spots.SpotsModel attribute) (piscis.networks.conv.SqueezeExcite attribute) smoothf1_loss() (in module piscis.losses) snap_coords() (in module piscis.utils) split (piscis.data.MultiSpotsDataset attribute) (piscis.data.SpotsDataset attribute) SpotsDataset (class in piscis.data) SpotsDataStream (class in piscis.data) SpotsModel (class in piscis.models.spots) SqueezeExcite (class in piscis.networks.conv) stage_sizes (piscis.networks.efficientnetv2.EfficientNetV2 attribute) (piscis.networks.fpn.Decoder attribute) standardize() (in module piscis.transforms) stem (piscis.networks.efficientnetv2.EfficientNetV2 attribute) stochastic_depth (piscis.networks.conv.FusedMBConv attribute) (piscis.networks.conv.MBConv attribute) style (piscis.networks.fpn.FPN attribute) T train_epoch() (in module piscis.training) train_model() (in module piscis.training) U up_blocks (piscis.networks.fpn.Decoder attribute) UpConv (class in piscis.networks.fpn) upsample (piscis.networks.fpn.Decoder attribute) use_res_connect (piscis.networks.conv.FusedMBConv attribute) (piscis.networks.conv.MBConv attribute) V val_epoch() (in module piscis.training) vmap_deformable_max_pool (in module piscis.utils) vmap_deformable_softmax_pool (in module piscis.utils) vmap_deformable_sum_pool (in module piscis.utils) vmap_peak_local_softmax (in module piscis.utils) voronoi_transform() (in module piscis.transforms) W WeightedDatasetSampler (class in piscis.data) weights (piscis.data.MultiSpotsDataset attribute) (piscis.data.WeightedDatasetSampler attribute) wrap_loss_fn() (in module piscis.losses) X x_paths (piscis.data.SpotsDataset attribute) Y y_paths (piscis.data.SpotsDataset attribute)
