Index

A

add_inset() (in module nstm.viz_utils) add_scalebar() (in module nstm.viz_utils) annealed_epoch (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute)

AnnealedHashEmbedding (class in nstm.hash_encoding) AnnealedPosenc (class in nstm.pos_encoding) apo_filter (nstm.sim3d_flow.FluoSIM3D attribute) apodization() (in module nstm.utils) apodize_edge() (in module nstm.utils)

B

base_resolution (nstm.hash_encoding.HashParameters attribute) bilinear_interp() (in module nstm.hash_encoding)

bounding_box (nstm.hash_encoding.HashParameters attribute) brownian() (in module nstm.utils)

C

color_coded_projection() (in module nstm.viz_utils)

cut_patches() (in module nstm.commands.full_to_patches)

D

Datasets (class in nstm.datasets) define_flags() (in module nstm.commands.czi_conversion) (in module nstm.commands.full_to_patches) (in module nstm.commands.process_raw_images) (in module nstm.commands.timestamp_generation) (in module nstm.diffcam_utils) (in module nstm.sim3d_utils) define_model() (in module nstm.sim3d_main) define_training_params() (in module nstm.sim3d_main)

DiffuserCamRSFlow (class in nstm.diffcam_flow) DiffuserCanRS (class in nstm.diffcam_flow) dim (nstm.pos_encoding.AnnealedPosenc attribute) dim_yx (nstm.diffcam_flow.DiffuserCanRS attribute) (nstm.utils.SystemParameters attribute) dim_zyx (nstm.utils.SystemParameters3D attribute) downsample_t (nstm.diffcam_flow.DiffuserCanRS attribute) DPC (class in nstm.dpc_flow) dpc_tikhonov_solver() (in module nstm.dpc_utils) DPCFlow (class in nstm.dpc_flow)

E

efficient() (nstm.diffcam_flow.DiffuserCanRS method)

encoding_at_level() (nstm.hash_encoding.HashEmbedding method) estimate_mod_illum() (in module nstm.sim3d_utils)

F

finest_resolution (nstm.hash_encoding.HashParameters attribute)

FluoSIM3D (class in nstm.sim3d_flow) FluoSIM3DWrapper (class in nstm.sim3d_flow)

G

gen_dampen_order0_mask() (in module nstm.sim3d_utils) gen_indicator() (in module nstm.diffcam_utils) gen_l2_reg_absorp() (in module nstm.dpc_flow) gen_l2_reg_phase() (in module nstm.dpc_flow) gen_loss_l2() (in module nstm.diffcam_flow) (in module nstm.dpc_flow) (in module nstm.sim3d_flow) gen_loss_l2_row() (in module nstm.diffcam_flow) gen_loss_l2_stack() (in module nstm.sim3d_flow) gen_loss_nonneg_reg() (in module nstm.sim3d_flow) gen_nonneg_reg() (in module nstm.diffcam_flow) gen_transfer_func() (in module nstm.dpc_utils) generate_affine_motion() (in module nstm.utils) generate_bead_phantom() (nstm.utils.PhantomTemporal method) generate_dense_yx_coords() (in module nstm.spacetime) generate_dense_zyx_coords() (in module nstm.spacetime) generate_exp() (in module nstm.sim3d_utils) generate_linear_motion() (in module nstm.utils)

generate_rod_phantom() (in module nstm.utils) generate_shepp_logan() (nstm.utils.PhantomTemporal method) generate_shepp_logan_2channel() (nstm.utils.PhantomTemporal method) generate_shepp_logan_affine() (nstm.utils.PhantomTemporal method) generate_shepp_logan_swirl() (nstm.utils.PhantomTemporal method) generate_sinusoidal() (in module nstm.sim3d_utils) generate_usaf_target() (nstm.utils.PhantomTemporal method) generate_usaf_target_affine() (nstm.utils.PhantomTemporal method) generate_usaf_target_shear() (nstm.utils.PhantomTemporal method) generate_usaf_target_swirl() (nstm.utils.PhantomTemporal method) genMeasurmentsLinear() (in module nstm.dpc_utils) genSourceAngular() (in module nstm.dpc_utils) get_modamp() (in module nstm.sim3d_utils) get_motion_map() (nstm.spacetime.SpaceTimeMLP method) get_no_overlap_mask_2d() (in module nstm.commands.full_to_patches) get_otf() (in module nstm.sim3d_utils) get_pixel_vertices() (in module nstm.hash_encoding) get_trajectory() (in module nstm.spacetime)

H

hash_fn() (in module nstm.hash_encoding) hash_param (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) hash_param_space (nstm.hash_encoding.HashEmbeddingTime attribute) hash_param_spacetime (nstm.hash_encoding.HashEmbeddingTimeCombined attribute)

hash_param_time (nstm.hash_encoding.HashEmbeddingTime attribute) HashEmbedding (class in nstm.hash_encoding) HashEmbeddingTime (class in nstm.hash_encoding) HashEmbeddingTimeCombined (class in nstm.hash_encoding) HashParameters (class in nstm.hash_encoding) hotpixel_removal() (in module nstm.utils)

I

image_resizing() (in module nstm.datasets)

image_upsampling() (in module nstm.datasets) init_uniform_std (nstm.hash_encoding.HashParameters attribute)

K

k0angles (nstm.sim3d_utils.SIMParameter3D attribute)

kernel_init() (nstm.spacetime.MLP method) (nstm.spacetime.MLPParameters method)

L

line_spacing (nstm.sim3d_utils.SIMParameter3D attribute) linear_interp() (in module nstm.hash_encoding) list() (nstm.datasets.Datasets method) list_files() (nstm.datasets.SIM3DDataLoaderMultitime method) list_source (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) load() (nstm.datasets.Datasets method) load_3DSIM_OTF() (nstm.datasets.SIM3DDataLoader method)

load_3DSIM_raw() (nstm.datasets.SIM3DDataLoader method) (nstm.datasets.SIM3DDataLoaderMultitime method) load_data_psf() (in module nstm.diffcam_utils) load_illum_pattern() (in module nstm.dpc_utils) load_metadata() (nstm.datasets.SIM3DDataLoader method) load_OTF() (nstm.datasets.SIM3DDataLoader static method) load_video() (in module nstm.utils) log2_hashmap_size (nstm.hash_encoding.HashParameters attribute)

M

main() (in module nstm.commands.czi_conversion) (in module nstm.commands.full_to_patches) (in module nstm.commands.process_raw_images) (in module nstm.commands.timestamp_generation) (in module nstm.diffcam_main) (in module nstm.sim3d_main) make_overlaps() (in module nstm.sim3d_utils) mean_background_amp (nstm.utils.SystemParameters attribute) merge_yx() (in module nstm.commands.full_to_patches) meta_path (nstm.datasets.SIM3DDataLoader attribute) MLP (class in nstm.spacetime) MLPParameters (class in nstm.spacetime) module nstm nstm.commands nstm.commands.czi_conversion nstm.commands.full_to_patches nstm.commands.process_raw_images nstm.commands.timestamp_generation nstm.datasets nstm.diffcam_flow nstm.diffcam_main nstm.diffcam_utils nstm.dpc_flow nstm.dpc_utils nstm.hash_encoding nstm.pos_encoding nstm.sim3d_flow nstm.sim3d_main nstm.sim3d_utils nstm.spacetime nstm.utils nstm.viz_utils

motion_embedding (nstm.spacetime.SpaceTimeParameters attribute) motion_embedding_param (nstm.spacetime.SpaceTimeParameters attribute) motion_mlp_param (nstm.spacetime.SpaceTimeParameters attribute)

N

n_features_per_level (nstm.hash_encoding.HashParameters attribute) n_input_features (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) n_levels (nstm.hash_encoding.HashParameters attribute) na (nstm.utils.SystemParameters attribute) (nstm.utils.SystemParameters3D attribute) name (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.diffcam_flow.DiffuserCanRS attribute) (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) (nstm.hash_encoding.HashEmbeddingTime attribute) (nstm.hash_encoding.HashEmbeddingTimeCombined attribute) (nstm.pos_encoding.AnnealedPosenc attribute) (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.FluoSIM3DWrapper attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) (nstm.spacetime.MLP attribute) (nstm.spacetime.SpaceTimeMLP attribute) ndirs (nstm.datasets.SIM3DDataLoader attribute) (nstm.sim3d_utils.SIMParameter3D attribute) net_activation (nstm.spacetime.MLP attribute) (nstm.spacetime.MLPParameters attribute) net_depth (nstm.spacetime.MLP attribute) (nstm.spacetime.MLPParameters attribute) net_width (nstm.spacetime.MLP attribute) (nstm.spacetime.MLPParameters attribute) nlines (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.diffcam_flow.DiffuserCanRS attribute) notch_filter() (in module nstm.utils) nphases (nstm.datasets.SIM3DDataLoader attribute) (nstm.sim3d_utils.SIMParameter3D attribute) nstm module nstm.commands module nstm.commands.czi_conversion module

nstm.commands.full_to_patches module nstm.commands.process_raw_images module nstm.commands.timestamp_generation module nstm.datasets module nstm.diffcam_flow module nstm.diffcam_main module nstm.diffcam_utils module nstm.dpc_flow module nstm.dpc_utils module nstm.hash_encoding module nstm.pos_encoding module nstm.sim3d_flow module nstm.sim3d_main module nstm.sim3d_utils module nstm.spacetime module nstm.utils module nstm.viz_utils module num_freqs (nstm.pos_encoding.PosencParameters attribute) num_output_channels (nstm.spacetime.MLP attribute) (nstm.spacetime.SpaceTimeMLP attribute) num_timepoint (nstm.datasets.SIM3DDataLoaderMultitime attribute)

O

object_embedding (nstm.spacetime.SpaceTimeParameters attribute) object_embedding_param (nstm.spacetime.SpaceTimeParameters attribute) object_mlp_param (nstm.spacetime.SpaceTimeParameters attribute) object_transform() (in module nstm.utils) object_transform_affine() (in module nstm.utils) object_transform_swirl() (in module nstm.utils) optical_param (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.FluoSIM3DWrapper attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) (nstm.spacetime.SpaceTimeMLP attribute)

order0_grad_reduction (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) origin_pixel_offset_yx (nstm.sim3d_utils.SIMParameter3D attribute) OTF (nstm.sim3d_utils.SIMParameter3D attribute) OTF_3D_fluo() (in module nstm.utils) otf_path (nstm.datasets.SIM3DDataLoader attribute) otf_support_mask() (in module nstm.sim3d_utils) out_activation (nstm.spacetime.SpaceTimeParameters attribute)

P

padding_yx (nstm.utils.SystemParameters attribute) padding_zyx (nstm.utils.SystemParameters3D attribute) param_dtype (nstm.spacetime.MLP attribute) parent (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.diffcam_flow.DiffuserCanRS attribute) (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) (nstm.hash_encoding.HashEmbeddingTime attribute) (nstm.hash_encoding.HashEmbeddingTimeCombined attribute) (nstm.pos_encoding.AnnealedPosenc attribute) (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.FluoSIM3DWrapper attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) (nstm.spacetime.MLP attribute) (nstm.spacetime.SpaceTimeMLP attribute) PhantomTemporal (class in nstm.utils) phase_only (nstm.dpc_flow.DPCFlow attribute)

pixel_size (nstm.utils.SystemParameters attribute) (nstm.utils.SystemParameters3D attribute) pixel_size_z (nstm.utils.SystemParameters3D attribute) posenc_max (nstm.pos_encoding.PosencParameters attribute) posenc_min (nstm.pos_encoding.PosencParameters attribute) posenc_param (nstm.pos_encoding.AnnealedPosenc attribute) PosencParameters (class in nstm.pos_encoding) precision (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) (nstm.hash_encoding.HashEmbeddingTime attribute) (nstm.hash_encoding.HashEmbeddingTimeCombined attribute) (nstm.spacetime.MLP attribute) (nstm.spacetime.SpaceTimeMLP attribute) precision_to_dtype() (in module nstm.hash_encoding) psf (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.diffcam_flow.DiffuserCanRS attribute) psf_gaussian_approx() (in module nstm.utils)

Q

quadrilinear_interp() (in module nstm.hash_encoding)

R

rad_avg_OTF_expansion() (in module nstm.sim3d_utils) ram_efficient (nstm.diffcam_flow.DiffuserCamRSFlow attribute) replace() (nstm.hash_encoding.HashParameters method) (nstm.pos_encoding.PosencParameters method) (nstm.sim3d_utils.SIMParameter3D method) (nstm.spacetime.MLPParameters method) (nstm.spacetime.SpaceTimeParameters method) (nstm.utils.SystemParameters method) (nstm.utils.SystemParameters3D method)

RI_medium (nstm.utils.SystemParameters attribute) (nstm.utils.SystemParameters3D attribute)

S

scope (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.diffcam_flow.DiffuserCanRS attribute) (nstm.dpc_flow.DPC attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.hash_encoding.AnnealedHashEmbedding attribute) (nstm.hash_encoding.HashEmbedding attribute) (nstm.hash_encoding.HashEmbeddingTime attribute) (nstm.hash_encoding.HashEmbeddingTimeCombined attribute) (nstm.pos_encoding.AnnealedPosenc attribute) (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.FluoSIM3DWrapper attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) (nstm.spacetime.MLP attribute) (nstm.spacetime.SpaceTimeMLP attribute) separate_bands() (in module nstm.sim3d_utils) setup() (nstm.diffcam_flow.DiffuserCamRSFlow method) (nstm.diffcam_flow.DiffuserCanRS method) (nstm.dpc_flow.DPC method) (nstm.dpc_flow.DPCFlow method) (nstm.hash_encoding.AnnealedHashEmbedding method) (nstm.hash_encoding.HashEmbedding method) (nstm.hash_encoding.HashEmbeddingTime method) (nstm.hash_encoding.HashEmbeddingTimeCombined method) (nstm.sim3d_flow.FluoSIM3D method) (nstm.sim3d_flow.FluoSIM3DWrapper method) (nstm.sim3d_flow.SIM3DSpacetime method) (nstm.spacetime.SpaceTimeMLP method)

SIM3DDataLoader (class in nstm.datasets) SIM3DDataLoaderMultitime (class in nstm.datasets) SIM3DSpacetime (class in nstm.sim3d_flow) sim_param (nstm.sim3d_flow.FluoSIM3D attribute) (nstm.sim3d_flow.FluoSIM3DWrapper attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) SIMParameter3D (class in nstm.sim3d_utils) skip_layer (nstm.spacetime.MLP attribute) (nstm.spacetime.MLPParameters attribute) sourceGen() (in module nstm.dpc_utils) spacetime_param (nstm.diffcam_flow.DiffuserCamRSFlow attribute) (nstm.dpc_flow.DPCFlow attribute) (nstm.sim3d_flow.SIM3DSpacetime attribute) (nstm.spacetime.SpaceTimeMLP attribute) SpaceTimeMLP (class in nstm.spacetime) SpaceTimeParameters (class in nstm.spacetime) start_timepoint (nstm.datasets.SIM3DDataLoader attribute) starting_phases (nstm.sim3d_utils.SIMParameter3D attribute) SystemParameters (class in nstm.utils) SystemParameters3D (class in nstm.utils)

T

trilinear_interp() (in module nstm.hash_encoding)

U

update_flags() (in module nstm.utils)

V

volume() (in module nstm.viz_utils)

volume4d() (in module nstm.viz_utils)

W

wavelength (nstm.utils.SystemParameters attribute) (nstm.utils.SystemParameters3D attribute)

wavelength_exc (nstm.utils.SystemParameters attribute) (nstm.utils.SystemParameters3D attribute)

Z

zoomfact (nstm.datasets.SIM3DDataLoader attribute)