Index

A

add_audio() (decode.neuralfitter.utils.logger.NoLog method) add_custom_scalars() (decode.neuralfitter.utils.logger.NoLog method) add_embedding() (decode.neuralfitter.utils.logger.NoLog method) add_figure() (decode.neuralfitter.utils.logger.NoLog method) add_figures() (decode.neuralfitter.utils.logger.NoLog method) add_graph() (decode.neuralfitter.utils.logger.NoLog method) add_histogram() (decode.neuralfitter.utils.logger.NoLog method) add_hparams() (decode.neuralfitter.utils.logger.NoLog method) add_image() (decode.neuralfitter.utils.logger.NoLog method) add_images() (decode.neuralfitter.utils.logger.NoLog method) add_mesh() (decode.neuralfitter.utils.logger.NoLog method) add_pr_curve() (decode.neuralfitter.utils.logger.NoLog method) add_root_relative() (in module decode.utils.param_io) add_scalar() (decode.neuralfitter.utils.logger.DictLogger method) (decode.neuralfitter.utils.logger.NoLog method) add_scalar_dict() (decode.neuralfitter.utils.logger.DictLogger method) (decode.neuralfitter.utils.logger.NoLog method) (decode.neuralfitter.utils.logger.SummaryWriter method) add_scalars() (decode.neuralfitter.utils.logger.NoLog method)

add_text() (decode.neuralfitter.utils.logger.NoLog method) add_video() (decode.neuralfitter.utils.logger.NoLog method) alpha_ax (decode.evaluation.evaluation.SMLMEvaluation attribute) alpha_lat (decode.evaluation.evaluation.SMLMEvaluation attribute) AmplitudeRescale (class in decode.neuralfitter.scale_transform) apply_detection_nonlin() (decode.neuralfitter.models.model_param.DoubleMUnet method) (decode.neuralfitter.models.model_speced_impl.SigmaMUNet method) apply_nonlin() (decode.neuralfitter.models.model_param.DoubleMUnet method) (decode.neuralfitter.models.model_param.SimpleSMLMNet method) (decode.neuralfitter.models.model_speced_impl.SigmaMUNet method) apply_pnl() (decode.neuralfitter.models.model_param.SimpleSMLMNet method) area (decode.simulation.structure_prior.RandomStructure property) (decode.simulation.structure_prior.StructurePrior property) astigmatism() (decode.simulation.psf_kernel.GaussianPSF static method) at_least_one_dim() (in module decode.generic.emitter) AutoCenterCrop (class in decode.neuralfitter.frame_processing) autofill_dict() (in module decode.utils.param_io) AutoPad (class in decode.neuralfitter.frame_processing) autoset_scaling() (in module decode.utils.param_io) avg (decode.evaluation.utils.MetricMeter property)

B

Background (class in decode.simulation.background) backward() (decode.simulation.camera.Camera method) (decode.simulation.camera.Photon2Camera method) BatchFileLoader (class in decode.utils.frames_io) bg_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute)

bg_scr (decode.generic.emitter.EmitterSet property) BgPerEmitterFromBgFrame (class in decode.simulation.background) bin_ctr_x (decode.simulation.psf_kernel.DeltaPSF property) bin_ctr_y (decode.simulation.psf_kernel.DeltaPSF property) binom_pdiverse() (in module decode.neuralfitter.utils.probability)

C

calc_gaussians() (decode.renderer.renderer.RendererIndividual2D method) Camera (class in decode.simulation.camera) cat() (decode.generic.emitter.EmitterSet static method) cdf_get() (decode.neuralfitter.de_bias.UniformizeOffset method) ch_out (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) check_file() (in module decode.utils.loader) check_forward_sanity() (decode.neuralfitter.weight_generator.SimpleWeight method) (decode.neuralfitter.weight_generator.WeightGenerator method) check_load() (in module decode.utils.loader) check_sanity() (decode.neuralfitter.weight_generator.SimpleWeight method) (decode.simulation.camera.SCMOS method) check_target() (decode.neuralfitter.models.model_param.SimpleSMLMNet static method) CheckPoint (class in decode.utils.checkpoint) chunks() (decode.generic.emitter.EmitterSet method) clean_emitter() (decode.generic.process.RemoveOutOfFOV method) clone() (decode.generic.emitter.EmitterSet method) connect_point_set() (in module decode.plot.frame_coord)

ConsistencyPostprocessing (class in decode.neuralfitter.post_processing) const_roi_target() (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget method) convert_param_debug() (decode.utils.param_io.ParamHandling static method) convert_param_file() (decode.utils.param_io.ParamHandling method) coord2impl() (decode.simulation.psf_kernel.CubicSplinePSF method) CoordinateOnlyEmitter (class in decode.generic.emitter) copy_pkg_file() (in module decode.utils.notebooks) copy_reference_param() (in module decode.utils.param_io) count (decode.evaluation.utils.MetricMeter property) cpu() (decode.simulation.psf_kernel.CubicSplinePSF method) crlb() (decode.simulation.psf_kernel.CubicSplinePSF method) (decode.simulation.psf_kernel.PSF method) crlb_sq() (decode.simulation.psf_kernel.CubicSplinePSF method) CubicSplinePSF (class in decode.simulation.psf_kernel) cuda() (decode.simulation.psf_kernel.CubicSplinePSF method) cuda_compiled (decode.simulation.psf_kernel.CubicSplinePSF property) cuda_is_available() (decode.simulation.psf_kernel.CubicSplinePSF static method)

D

data (decode.generic.emitter.EmitterSet property) decode module decode.evaluation module decode.evaluation.evaluation module decode.evaluation.match_emittersets module decode.evaluation.metric module decode.evaluation.predict_dist module decode.evaluation.utils module decode.generic module decode.generic.emitter module decode.generic.process module decode.generic.slicing module decode.generic.test_utils module decode.neuralfitter module decode.neuralfitter.coord_transform module decode.neuralfitter.dataset module decode.neuralfitter.de_bias module decode.neuralfitter.em_filter module decode.neuralfitter.frame_processing module decode.neuralfitter.inference module decode.neuralfitter.inference.inference module decode.neuralfitter.inference.pred_tif module decode.neuralfitter.models module decode.neuralfitter.models.model_param module decode.neuralfitter.models.model_speced_impl module decode.neuralfitter.models.unet_param module decode.neuralfitter.models.unet_parts module decode.neuralfitter.post_processing module decode.neuralfitter.sampling module decode.neuralfitter.scale_transform module decode.neuralfitter.target_generator module decode.neuralfitter.train module decode.neuralfitter.train.live_engine module decode.neuralfitter.train.random_simulation module decode.neuralfitter.train_val_impl module decode.neuralfitter.utils module decode.neuralfitter.utils.last_layer_dynamics module decode.neuralfitter.utils.log_train_val_progress module decode.neuralfitter.utils.logger module

decode.neuralfitter.utils.padding_calc module decode.neuralfitter.utils.probability module decode.neuralfitter.utils.processing module decode.neuralfitter.weight_generator module decode.plot module decode.plot.fancy_plot module decode.plot.frame_coord module decode.renderer module decode.renderer.renderer module decode.simulation module decode.simulation.background module decode.simulation.camera module decode.simulation.emitter_generator module decode.simulation.noise_distributions module decode.simulation.psf_kernel module decode.simulation.simulator module decode.simulation.structure_prior module decode.utils module decode.utils.bookkeeping module decode.utils.calibration_io module decode.utils.checkpoint module decode.utils.emitter_io module decode.utils.emitter_trafo module decode.utils.example_helper module decode.utils.frames_io module decode.utils.loader module decode.utils.model_io module decode.utils.notebooks module decode.utils.param_io module decode.utils.types module decode_state() (in module decode.utils.bookkeeping) DeltaPSF (class in decode.simulation.psf_kernel) derivative() (decode.simulation.psf_kernel.CubicSplinePSF method) descriptors (decode.evaluation.evaluation.SMLMEvaluation attribute) deviation_dist() (in module decode.evaluation.predict_dist) dict (decode.utils.checkpoint.CheckPoint property) DictLogger (class in decode.neuralfitter.utils.logger) dim() (decode.generic.emitter.EmitterSet method) DisableAttributes (class in decode.neuralfitter.target_generator) dist_vol (decode.evaluation.match_emittersets.GreedyHungarianMatching attribute) DistanceEvaluation (class in decode.evaluation.evaluation) double_conv (class in decode.neuralfitter.models.unet_parts) DoubleMUnet (class in decode.neuralfitter.models.model_param) down (class in decode.neuralfitter.models.unet_parts) down_3d (class in decode.neuralfitter.models.unet_parts) dump() (decode.utils.checkpoint.CheckPoint method)

E

effcy_ax (decode.evaluation.evaluation.SMLMEvaluation property) effcy_lat (decode.evaluation.evaluation.SMLMEvaluation property) effcy_vol (decode.evaluation.evaluation.SMLMEvaluation property) efficiency() (in module decode.evaluation.metric) em_avg (decode.simulation.emitter_generator.EmitterSamplerFrameIndependent property) emitter (decode.neuralfitter.dataset.SMLMAPrioriDataset property) emitter_deviations() (in module decode.evaluation.predict_dist) EmitterFilter (class in decode.neuralfitter.em_filter) EmitterMatcher (class in decode.evaluation.match_emittersets)

EmitterPopperMultiFrame (class in decode.simulation.emitter_generator) EmitterPopperSingle (class in decode.simulation.emitter_generator) EmitterSampler (class in decode.simulation.emitter_generator) EmitterSamplerBlinking (class in decode.simulation.emitter_generator) EmitterSamplerFrameIndependent (class in decode.simulation.emitter_generator) EmitterSet (class in decode.generic.emitter) EmitterWriteStream (class in decode.utils.emitter_io) EmptyEmitterSet (class in decode.generic.emitter) eq_attr() (decode.generic.emitter.EmitterSet method) evaluate() (decode.neuralfitter.inference.pred_tif.PredictEval method)

F

file_extensions (decode.utils.param_io.ParamHandling attribute) file_loadable() (in module decode.generic.test_utils) filter() (decode.evaluation.match_emittersets.GreedyHungarianMatching method) filter_by_sigma() (decode.generic.emitter.EmitterSet method) fisher() (decode.simulation.psf_kernel.CubicSplinePSF method) forward() (decode.evaluation.evaluation.DistanceEvaluation method) (decode.evaluation.evaluation.SegmentationEvaluation method) (decode.evaluation.evaluation.SMLMEvaluation method) (decode.evaluation.evaluation.WeightedErrors method) (decode.evaluation.match_emittersets.EmitterMatcher method) (decode.evaluation.match_emittersets.GreedyHungarianMatching method) (decode.generic.process.Identity static method) (decode.generic.process.ProcessEmitters method) (decode.generic.process.RemoveOutOfFOV method) (decode.neuralfitter.coord_transform.Offset2Coordinate method) (decode.neuralfitter.de_bias.UniformizeOffset method) (decode.neuralfitter.em_filter.EmitterFilter method) (decode.neuralfitter.em_filter.NoEmitterFilter method) (decode.neuralfitter.em_filter.PhotonFilter method) (decode.neuralfitter.em_filter.TarEmitterFilter method) (decode.neuralfitter.frame_processing.AutoCenterCrop method) (decode.neuralfitter.frame_processing.AutoPad method) (decode.neuralfitter.frame_processing.FrameProcessing method) (decode.neuralfitter.frame_processing.Mirror2D method) (decode.neuralfitter.inference.inference.Infer method) (decode.neuralfitter.inference.inference.LiveInfer method) (decode.neuralfitter.inference.pred_tif.PredictEval method) (decode.neuralfitter.models.model_param.DoubleMUnet method) (decode.neuralfitter.models.model_param.MLTHeads method) (decode.neuralfitter.models.model_param.SimpleSMLMNet method) (decode.neuralfitter.models.model_speced_impl.SigmaMUNet method) (decode.neuralfitter.models.unet_param.UNetBase method) (decode.neuralfitter.models.unet_param.Upsample method) (decode.neuralfitter.models.unet_parts.double_conv method) (decode.neuralfitter.models.unet_parts.down method) (decode.neuralfitter.models.unet_parts.inconv method) (decode.neuralfitter.models.unet_parts.outconv method) (decode.neuralfitter.models.unet_parts.up method) (decode.neuralfitter.models.unet_parts.Upsample method) (decode.neuralfitter.post_processing.ConsistencyPostprocessing method) (decode.neuralfitter.post_processing.LookUpPostProcessing method) (decode.neuralfitter.post_processing.NoPostProcessing method) (decode.neuralfitter.post_processing.PostProcessing method) (decode.neuralfitter.post_processing.SpatialIntegration method) (decode.neuralfitter.scale_transform.AmplitudeRescale method) (decode.neuralfitter.scale_transform.FourFoldInverseOffsetRescale method) (decode.neuralfitter.scale_transform.InverseOffsetRescale method) (decode.neuralfitter.scale_transform.InverseParamListRescale method) (decode.neuralfitter.scale_transform.OffsetRescale method) (decode.neuralfitter.scale_transform.ParameterListRescale method) (decode.neuralfitter.scale_transform.SpatialInterpolation method) (decode.neuralfitter.target_generator.DisableAttributes method) (decode.neuralfitter.target_generator.FourFoldEmbedding method) (decode.neuralfitter.target_generator.ParameterListTarget method) (decode.neuralfitter.target_generator.TargetGenerator method) (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget method) (decode.neuralfitter.utils.processing.ParallelTransformSequence method) (decode.neuralfitter.utils.processing.TransformSequence method) (decode.neuralfitter.weight_generator.FourFoldSimpleWeight method) (decode.neuralfitter.weight_generator.SimpleWeight method) (decode.neuralfitter.weight_generator.WeightGenerator method) (decode.renderer.renderer.Renderer method) (decode.renderer.renderer.Renderer2D method) (decode.simulation.background.Background method) (decode.simulation.background.BgPerEmitterFromBgFrame method) (decode.simulation.camera.Camera method) (decode.simulation.camera.Photon2Camera method) (decode.simulation.camera.SCMOS method) (decode.simulation.noise_distributions.Gamma method) (decode.simulation.noise_distributions.Gaussian method) (decode.simulation.noise_distributions.NoiseDistribution method) (decode.simulation.noise_distributions.Poisson method) (decode.simulation.noise_distributions.ZeroNoise method) (decode.simulation.psf_kernel.CubicSplinePSF method) (decode.simulation.psf_kernel.DeltaPSF method) (decode.simulation.psf_kernel.GaussianPSF method) (decode.simulation.psf_kernel.PSF method) (decode.simulation.simulator.Simulation method)

forward_() (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget method) forward_on_sampled_sensor_window() (decode.simulation.camera.SCMOS method) forward_parts() (decode.neuralfitter.models.unet_param.UNetBase method) forward_raw() (decode.neuralfitter.inference.pred_tif.PredictEval method) forward_rois() (decode.simulation.psf_kernel.CubicSplinePSF method) FourFoldEmbedding (class in decode.neuralfitter.target_generator) FourFoldInverseOffsetRescale (class in decode.neuralfitter.scale_transform) FourFoldSimpleWeight (class in decode.neuralfitter.weight_generator) frame2roi_coord() (decode.simulation.psf_kernel.CubicSplinePSF method) FrameProcessing (class in decode.neuralfitter.frame_processing)

G

Gamma (class in decode.simulation.noise_distributions) Gaussian (class in decode.simulation.noise_distributions) GaussianPSF (class in decode.simulation.psf_kernel) get_activation() (in module decode.neuralfitter.models.unet_param) get_decode_meta() (in module decode.utils.emitter_io)

get_extent() (decode.renderer.renderer.Renderer2D method) get_frame_extent() (in module decode.neuralfitter.frame_processing) get_max_batch_size() (decode.neuralfitter.inference.inference.Infer static method) get_subset_frame() (decode.generic.emitter.EmitterSet method) GreedyHungarianMatching (class in decode.evaluation.match_emittersets)

H

hash_model() (in module decode.utils.model_io) hist() (decode.evaluation.utils.MetricMeter method)

hist_detection() (decode.generic.emitter.EmitterSet method) histedges_equal_n() (decode.neuralfitter.de_bias.UniformizeOffset method)

I

Identity (class in decode.generic.process) inconv (class in decode.neuralfitter.models.unet_parts) inconv_3d (class in decode.neuralfitter.models.unet_parts) Infer (class in decode.neuralfitter.inference.inference) InferenceDataset (class in decode.neuralfitter.dataset)

init_dataset() (decode.neuralfitter.inference.pred_tif.PredictEvalTif method) init_spline() (decode.utils.calibration_io.SMAPSplineCoefficient method) inv_default() (decode.simulation.psf_kernel.CubicSplinePSF method) InverseOffsetRescale (class in decode.neuralfitter.scale_transform) InverseParamListRescale (class in decode.neuralfitter.scale_transform) ix_split() (in module decode.generic.slicing)

K

kde_sorted() (in module decode.evaluation.utils)

keys() (decode.utils.types.RecursiveNamespace method)

L

live_engine_setup() (in module decode.neuralfitter.train.live_engine) LiveInfer (class in decode.neuralfitter.inference.inference) load() (decode.generic.emitter.EmitterSet static method) (decode.utils.checkpoint.CheckPoint class method) (in module decode.utils.loader) load_csv() (decode.neuralfitter.inference.pred_tif.PredictEvalTif static method) (in module decode.utils.emitter_io) load_example_package() (in module decode.utils.example_helper) load_examples() (in module decode.utils.notebooks) load_gateway() (in module decode.utils.example_helper) load_h5() (in module decode.utils.emitter_io) load_init() (decode.utils.model_io.LoadSaveModel method) load_params() (decode.utils.param_io.ParamHandling method) (in module decode.utils.param_io)

load_reference() (in module decode.utils.param_io) load_smap() (in module decode.utils.emitter_io) load_tif() (in module decode.utils.frames_io) load_tif_csv() (decode.neuralfitter.inference.pred_tif.PredictEvalTif method) load_torch() (in module decode.utils.emitter_io) LoadSaveModel (class in decode.utils.model_io) log_dists() (in module decode.neuralfitter.utils.log_train_val_progress) log_frames() (in module decode.neuralfitter.utils.log_train_val_progress) log_kpi() (in module decode.neuralfitter.utils.log_train_val_progress) log_train() (in module decode.neuralfitter.utils.log_train_val_progress) LookUpPostProcessing (class in decode.neuralfitter.post_processing) LooseEmitterSet (class in decode.generic.emitter)

M

map_entry() (decode.utils.types.RecursiveNamespace static method) mean (decode.evaluation.utils.MetricMeter property) meta (decode.generic.emitter.EmitterSet property) MetricMeter (class in decode.evaluation.utils) Mirror2D (class in decode.neuralfitter.frame_processing) MLTHeads (class in decode.neuralfitter.models.model_param) module decode decode.evaluation decode.evaluation.evaluation decode.evaluation.match_emittersets decode.evaluation.metric decode.evaluation.predict_dist decode.evaluation.utils decode.generic decode.generic.emitter decode.generic.process decode.generic.slicing decode.generic.test_utils decode.neuralfitter decode.neuralfitter.coord_transform decode.neuralfitter.dataset decode.neuralfitter.de_bias decode.neuralfitter.em_filter decode.neuralfitter.frame_processing decode.neuralfitter.inference decode.neuralfitter.inference.inference decode.neuralfitter.inference.pred_tif decode.neuralfitter.models decode.neuralfitter.models.model_param decode.neuralfitter.models.model_speced_impl decode.neuralfitter.models.unet_param decode.neuralfitter.models.unet_parts decode.neuralfitter.post_processing decode.neuralfitter.sampling decode.neuralfitter.scale_transform decode.neuralfitter.target_generator decode.neuralfitter.train decode.neuralfitter.train.live_engine decode.neuralfitter.train.random_simulation decode.neuralfitter.train_val_impl decode.neuralfitter.utils decode.neuralfitter.utils.last_layer_dynamics decode.neuralfitter.utils.log_train_val_progress decode.neuralfitter.utils.logger decode.neuralfitter.utils.padding_calc decode.neuralfitter.utils.probability decode.neuralfitter.utils.processing decode.neuralfitter.weight_generator decode.plot decode.plot.fancy_plot decode.plot.frame_coord decode.renderer decode.renderer.renderer decode.simulation decode.simulation.background decode.simulation.camera decode.simulation.emitter_generator decode.simulation.noise_distributions decode.simulation.psf_kernel decode.simulation.simulator decode.simulation.structure_prior decode.utils decode.utils.bookkeeping decode.utils.calibration_io decode.utils.checkpoint decode.utils.emitter_io decode.utils.emitter_trafo decode.utils.example_helper decode.utils.frames_io decode.utils.loader decode.utils.model_io decode.utils.notebooks decode.utils.param_io decode.utils.types

mt_heads (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) MultiLogger (class in decode.neuralfitter.utils.logger)

N

n_par (decode.simulation.psf_kernel.CubicSplinePSF attribute) NoEmitterFilter (class in decode.neuralfitter.em_filter) NoiseDistribution (class in decode.simulation.noise_distributions)

NoLog (class in decode.neuralfitter.utils.logger) NoPostProcessing (class in decode.neuralfitter.post_processing) norms (decode.neuralfitter.models.unet_param.UNetBase attribute) num_frames (decode.simulation.emitter_generator.EmitterSamplerBlinking property)

O

Offset2Coordinate (class in decode.neuralfitter.coord_transform) OffsetRescale (class in decode.neuralfitter.scale_transform) open_n_hash() (in module decode.generic.test_utils)

out_channels_heads (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) outconv (class in decode.neuralfitter.models.unet_parts) outsize_calc() (in module decode.neuralfitter.utils.padding_calc)

P

p_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) pad_same_calc() (in module decode.neuralfitter.utils.padding_calc) ParallelTransformSequence (class in decode.neuralfitter.utils.processing) ParameterListRescale (class in decode.neuralfitter.scale_transform) ParameterListTarget (class in decode.neuralfitter.target_generator) ParamHandling (class in decode.utils.param_io) parse() (decode.evaluation.match_emittersets.GreedyHungarianMatching class method) (decode.neuralfitter.coord_transform.Offset2Coordinate class method) (decode.neuralfitter.models.model_param.DoubleMUnet class method) (decode.neuralfitter.models.model_param.SimpleSMLMNet static method) (decode.neuralfitter.models.model_speced_impl.SigmaMUNet class method) (decode.neuralfitter.post_processing.ConsistencyPostprocessing class method) (decode.neuralfitter.scale_transform.AmplitudeRescale static method) (decode.neuralfitter.scale_transform.InverseOffsetRescale class method) (decode.neuralfitter.scale_transform.OffsetRescale static method) (decode.neuralfitter.scale_transform.ParameterListRescale class method) (decode.neuralfitter.target_generator.DisableAttributes class method) (decode.neuralfitter.target_generator.FourFoldEmbedding class method) (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget class method) (decode.neuralfitter.utils.processing.TransformSequence class method) (decode.neuralfitter.weight_generator.FourFoldSimpleWeight class method) (decode.neuralfitter.weight_generator.SimpleWeight class method) (decode.neuralfitter.weight_generator.WeightGenerator class method) (decode.simulation.background.UniformBackground static method) (decode.simulation.camera.PerfectCamera class method) (decode.simulation.camera.Photon2Camera class method) (decode.simulation.emitter_generator.EmitterSamplerBlinking class method) (decode.simulation.structure_prior.RandomStructure class method) parse_args() (in module decode.neuralfitter.train.live_engine) (in module decode.utils.notebooks)

PerfectCamera (class in decode.simulation.camera) phot_scr (decode.generic.emitter.EmitterSet property) Photon2Camera (class in decode.simulation.camera) photon_range (decode.simulation.emitter_generator.EmitterSamplerFrameIndependent attribute) PhotonFilter (class in decode.neuralfitter.em_filter) plot() (decode.plot.frame_coord.PlotCoordinates method) (decode.plot.frame_coord.PlotCoordinates3D method) (decode.plot.frame_coord.PlotFrame method) (decode.plot.frame_coord.PlotFrameCoord method) plot_crosshair() (in module decode.plot.fancy_plot) plot_error() (decode.evaluation.evaluation.WeightedErrors static method) PlotCoordinates (class in decode.plot.frame_coord) PlotCoordinates3D (class in decode.plot.frame_coord) PlotFrame (class in decode.plot.frame_coord) PlotFrameCoord (class in decode.plot.frame_coord) Poisson (class in decode.simulation.noise_distributions) pool_modules (decode.neuralfitter.models.unet_param.UNetBase attribute) populate_crlb() (decode.generic.emitter.EmitterSet method) post_process_log_test() (in module decode.neuralfitter.utils.log_train_val_progress) PostProcessing (class in decode.neuralfitter.post_processing) precision_recall_jaccard() (in module decode.evaluation.metric) PredictEval (class in decode.neuralfitter.inference.pred_tif) PredictEvalSimulation (class in decode.neuralfitter.inference.pred_tif) PredictEvalTif (class in decode.neuralfitter.inference.pred_tif) ProcessEmitters (class in decode.generic.process) PSF (class in decode.simulation.psf_kernel) px_pointer_dist() (in module decode.evaluation.predict_dist) pxyz_mu_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) pxyz_sig_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute)

R

RandomEmitterSet (class in decode.generic.emitter) RandomStructure (class in decode.simulation.structure_prior) RecursiveNamespace (class in decode.utils.types) reduction (decode.evaluation.evaluation.WeightedErrors attribute) remove_by_exclude() (decode.utils.frames_io.BatchFileLoader method) RemoveOutOfFOV (class in decode.generic.process) render() (decode.renderer.renderer.Renderer method) (decode.renderer.renderer.Renderer2D method) Renderer (class in decode.renderer.renderer)

Renderer2D (class in decode.renderer.renderer) RendererIndividual2D (class in decode.renderer.renderer) rescale_last_layer_grad() (decode.neuralfitter.models.model_param.DoubleMUnet method) (decode.neuralfitter.models.model_param.SimpleSMLMNet method) reset() (decode.evaluation.utils.MetricMeter method) return_em (decode.neuralfitter.dataset.SMLMDataset attribute) return_emitterset() (decode.generic.emitter.LooseEmitterSet method) return_inverse() (decode.neuralfitter.scale_transform.OffsetRescale method) rmse_mad_dist() (in module decode.evaluation.metric)

S

same_dim_tensor() (in module decode.generic.emitter) same_shape_tensor() (in module decode.generic.emitter) same_weights() (in module decode.generic.test_utils) sample() (decode.neuralfitter.dataset.SMLMAPrioriDataset method) (decode.neuralfitter.dataset.SMLMLiveDataset method) (decode.simulation.background.Background method) (decode.simulation.background.UniformBackground method) (decode.simulation.emitter_generator.EmitterSampler method) (decode.simulation.emitter_generator.EmitterSamplerBlinking method) (decode.simulation.emitter_generator.EmitterSamplerFrameIndependent method) (decode.simulation.simulator.Simulation method) (decode.simulation.structure_prior.RandomStructure method) (decode.simulation.structure_prior.StructurePrior method) sample_crop() (in module decode.neuralfitter.sampling) sample_like() (decode.simulation.background.Background method) sample_loose_emitter() (decode.simulation.emitter_generator.EmitterSamplerBlinking method) sample_n() (decode.simulation.emitter_generator.EmitterSamplerBlinking method) (decode.simulation.emitter_generator.EmitterSamplerFrameIndependent method) sample_sensor_window() (decode.simulation.camera.SCMOS method) sanity_check() (decode.generic.emitter.LooseEmitterSet method) (decode.neuralfitter.dataset.SMLMDataset method) (decode.neuralfitter.dataset.SMLMLiveDataset method) (decode.neuralfitter.post_processing.ConsistencyPostprocessing method) (decode.neuralfitter.post_processing.PostProcessing method) (decode.neuralfitter.target_generator.TargetGenerator method) (decode.simulation.background.Background method) (decode.simulation.psf_kernel.CubicSplinePSF method) save() (decode.generic.emitter.EmitterSet method) (decode.utils.checkpoint.CheckPoint method) (decode.utils.model_io.LoadSaveModel method) save_csv() (in module decode.utils.emitter_io) save_h5() (in module decode.utils.emitter_io) save_params() (in module decode.utils.param_io) save_torch() (in module decode.utils.emitter_io)

SCMOS (class in decode.simulation.camera) search_bin_index() (decode.simulation.psf_kernel.DeltaPSF method) SegmentationEvaluation (class in decode.evaluation.evaluation) set_p_aggregation() (decode.neuralfitter.post_processing.SpatialIntegration class method) setup_dataloader() (in module decode.neuralfitter.train.live_engine) setup_random_simulation() (in module decode.neuralfitter.train.random_simulation) setup_trainer() (in module decode.neuralfitter.train.live_engine) ship_device() (in module decode.neuralfitter.train_val_impl) sigma_eps_default (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) SigmaMUNet (class in decode.neuralfitter.models.model_speced_impl) sigmoid_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) SimpleSMLMNet (class in decode.neuralfitter.models.model_param) SimpleWeight (class in decode.neuralfitter.weight_generator) Simulation (class in decode.simulation.simulator) single_frame (decode.generic.emitter.EmitterSet property) single_px_target() (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget method) skip_if() (decode.neuralfitter.post_processing.ConsistencyPostprocessing method) (decode.neuralfitter.post_processing.PostProcessing method) SMAPSplineCoefficient (class in decode.utils.calibration_io) SMLMAPrioriDataset (class in decode.neuralfitter.dataset) SMLMDataset (class in decode.neuralfitter.dataset) SMLMEvaluation (class in decode.evaluation.evaluation) SMLMLiveDataset (class in decode.neuralfitter.dataset) SMLMLiveSampleDataset (class in decode.neuralfitter.dataset) SMLMStaticDataset (class in decode.neuralfitter.dataset) sort_by_frame() (decode.generic.emitter.EmitterSet method) sort_by_frame_() (decode.generic.emitter.EmitterSet method) SpatialIntegration (class in decode.neuralfitter.post_processing) SpatialInterpolation (class in decode.neuralfitter.scale_transform) split_in_frames() (decode.generic.emitter.EmitterSet method) split_sliceable() (in module decode.generic.slicing) std (decode.evaluation.utils.MetricMeter property) StructurePrior (class in decode.simulation.structure_prior) SummaryWriter (class in decode.neuralfitter.utils.logger)

T

t0_dist (decode.simulation.emitter_generator.EmitterSamplerBlinking attribute) tanh_ch_ix (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) TarEmitterFilter (class in decode.neuralfitter.em_filter) TargetGenerator (class in decode.neuralfitter.target_generator) te (decode.generic.emitter.LooseEmitterSet property) tens_almeq() (in module decode.generic.test_utils) test() (in module decode.neuralfitter.train_val_impl) TiffTensor (class in decode.utils.frames_io) to_dict() (decode.generic.emitter.EmitterSet method) (decode.utils.types.RecursiveNamespace method) train() (in module decode.neuralfitter.train_val_impl) training (decode.neuralfitter.models.model_param.DoubleMUnet attribute) (decode.neuralfitter.models.model_param.MLTHeads attribute) (decode.neuralfitter.models.model_param.SimpleSMLMNet attribute) (decode.neuralfitter.models.model_speced_impl.SigmaMUNet attribute) (decode.neuralfitter.models.unet_param.UNet2d attribute) (decode.neuralfitter.models.unet_param.UNetBase attribute) (decode.neuralfitter.models.unet_param.Upsample attribute) (decode.neuralfitter.models.unet_parts.double_conv attribute) (decode.neuralfitter.models.unet_parts.down attribute) (decode.neuralfitter.models.unet_parts.down_3d attribute) (decode.neuralfitter.models.unet_parts.inconv attribute) (decode.neuralfitter.models.unet_parts.inconv_3d attribute) (decode.neuralfitter.models.unet_parts.outconv attribute) (decode.neuralfitter.models.unet_parts.up attribute) (decode.neuralfitter.models.unet_parts.Upsample attribute)

transform_emitter() (in module decode.utils.emitter_trafo) TransformSequence (class in decode.neuralfitter.utils.processing)

U

UNet2d (class in decode.neuralfitter.models.unet_param) UNetBase (class in decode.neuralfitter.models.unet_param) UnifiedEmbeddingTarget (class in decode.neuralfitter.target_generator) UniformBackground (class in decode.simulation.background) uniformize() (decode.neuralfitter.de_bias.UniformizeOffset method)

UniformizeOffset (class in decode.neuralfitter.de_bias) up (class in decode.neuralfitter.models.unet_parts) update() (decode.evaluation.utils.MetricMeter method) (decode.utils.checkpoint.CheckPoint method) Upsample (class in decode.neuralfitter.models.unet_param) (class in decode.neuralfitter.models.unet_parts)

W

weight_by_gradient() (in module decode.neuralfitter.utils.last_layer_dynamics) weight_init() (decode.neuralfitter.models.model_speced_impl.SigmaMUNet static method) WeightedErrors (class in decode.evaluation.evaluation)

WeightGenerator (class in decode.neuralfitter.weight_generator) wrap_callable() (in module decode.neuralfitter.utils.processing) write() (decode.utils.emitter_io.EmitterWriteStream method) write_params() (decode.utils.param_io.ParamHandling method)

X

xextent (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget property) xy_target() (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget method) xyz_nm (decode.generic.emitter.EmitterSet property) xyz_px (decode.generic.emitter.EmitterSet property)

xyz_scr (decode.generic.emitter.EmitterSet property) xyz_scr_nm (decode.generic.emitter.EmitterSet property) xyz_scr_px (decode.generic.emitter.EmitterSet property) xyz_sig_tot_nm (decode.generic.emitter.EmitterSet property) xyz_sig_weighted_tot_nm (decode.generic.emitter.EmitterSet property)

Y

yextent (decode.neuralfitter.target_generator.UnifiedEmbeddingTarget property)

Z

ZeroNoise (class in decode.simulation.noise_distributions)