Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | V | W A analyze_labels() (in module sphero_vem.measure.pipeline) assign_cell() (in module sphero_vem.measure.voxel) B BaseConfig (class in sphero_vem.utils.config) bbox_expand() (in module sphero_vem.utils.misc) bincount_ubyte() (in module sphero_vem.segmentation.np.utils) border_mask() (in module sphero_vem.registration.cropping) build_rag() (in module sphero_vem.segmentation.cellpose.utils) C calc_surface_rag() (in module sphero_vem.segmentation.cellpose.utils) calculate_ap() (in module sphero_vem.segmentation.cellpose.evaluation) calculate_flows() (in module sphero_vem.segmentation.cellpose.core) calculate_masks() (in module sphero_vem.segmentation.cellpose.core) CellposeFinetuneConfig (class in sphero_vem.segmentation.cellpose.finetuning) CellposeFlowConfig (class in sphero_vem.segmentation.cellpose.core) CellposeLogger (class in sphero_vem.segmentation.cellpose.finetuning) CellposeMaskConfig (class in sphero_vem.segmentation.cellpose.core) check_isotropic() (in module sphero_vem.utils.misc) compute_raw_flows() (in module sphero_vem.segmentation.cellpose.core) config (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) create_ome_multiscales() (in module sphero_vem.utils.misc) create_pyramid() (in module sphero_vem.preprocessing) crop_to_valid() (in module sphero_vem.preprocessing) CustomJSONEncoder (class in sphero_vem.utils.misc) D da_to_device() (in module sphero_vem.utils.accelerator) da_to_host() (in module sphero_vem.utils.accelerator) default() (sphero_vem.utils.misc.CustomJSONEncoder method) denoise_image() (in module sphero_vem.denoising) denoise_stack() (in module sphero_vem.denoising) DenoisingConfig (class in sphero_vem.denoising) DenoisingStats (class in sphero_vem.denoising) detect_torch_device() (in module sphero_vem.utils.misc) dirname_from_spacing() (in module sphero_vem.utils.misc) downsample_posterior() (in module sphero_vem.segmentation.np.utils) downscale_tensor() (in module sphero_vem.preprocessing) E evaluate_segmentation() (in module sphero_vem.segmentation.cellpose.evaluation) F find_border_crop() (in module sphero_vem.registration.cropping) finetune_cellpose() (in module sphero_vem.segmentation.cellpose.finetuning) fit() (sphero_vem.segmentation.np.core.NanoparticleSegmentation method) flatten_for_save() (in module sphero_vem.utils.misc) forward() (sphero_vem.registration.core.ImageTransform method) from_config() (sphero_vem.utils.config.ProcessingStep class method) from_dict() (sphero_vem.utils.config.BaseConfig class method) (sphero_vem.utils.config.ProcessingStep class method) from_json() (sphero_vem.utils.config.BaseConfig class method) full_config() (sphero_vem.utils.config.BaseConfig method) G gaussian_edge_map() (in module sphero_vem.segmentation.cellpose.utils) get_mesh() (in module sphero_vem.measure.mesh) get_multiscales() (in module sphero_vem.utils.misc) gpu_dispatch() (in module sphero_vem.utils.accelerator) H hist_bg (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) hist_stack (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) I ImageTransform (class in sphero_vem.registration.core) integral_image() (in module sphero_vem.registration.cropping) L label_nanoparticles() (in module sphero_vem.segmentation.np.core) label_properties() (in module sphero_vem.measure.pipeline) LabelAnalysisConfig (class in sphero_vem.measure.pipeline) load() (sphero_vem.segmentation.np.core.NanoparticleSegmentation class method) LossDispatcher (class in sphero_vem.metrics) M manual() (sphero_vem.utils.config.ProcessingStep class method) match_predictions() (in module sphero_vem.segmentation.cellpose.utils) module sphero_vem.denoising sphero_vem.io sphero_vem.measure.distance sphero_vem.measure.fractal sphero_vem.measure.mesh sphero_vem.measure.pipeline sphero_vem.measure.sdf sphero_vem.measure.voxel sphero_vem.metrics sphero_vem.preprocessing sphero_vem.registration.core sphero_vem.registration.cropping sphero_vem.registration.transforms sphero_vem.segmentation.cellpose.core sphero_vem.segmentation.cellpose.evaluation sphero_vem.segmentation.cellpose.finetuning sphero_vem.segmentation.cellpose.utils sphero_vem.segmentation.np.core sphero_vem.segmentation.np.utils sphero_vem.utils.accelerator sphero_vem.utils.config sphero_vem.utils.misc N NanoparticleSegConfig (class in sphero_vem.segmentation.np.core) NanoparticleSegmentation (class in sphero_vem.segmentation.np.core) ncc_loss() (in module sphero_vem.metrics) nuclei_distance() (in module sphero_vem.measure.distance) P p_bg (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) p_np (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) p_stack (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) postprocess_flows() (in module sphero_vem.segmentation.cellpose.core) predict() (sphero_vem.segmentation.np.core.NanoparticleSegmentation method) processing_metadata() (sphero_vem.utils.config.BaseConfig method) ProcessingStep (class in sphero_vem.utils.config) props_fractal() (in module sphero_vem.measure.fractal) props_mesh() (in module sphero_vem.measure.mesh) props_sdf() (in module sphero_vem.measure.sdf) props_voxel() (in module sphero_vem.measure.voxel) R rag_to_df() (in module sphero_vem.segmentation.cellpose.utils) read_manifest() (in module sphero_vem.utils.misc) read_regionprops() (in module sphero_vem.measure.pipeline) rechunk_array() (in module sphero_vem.preprocessing) reconstruct_tuples() (in module sphero_vem.utils.misc) rect_sum() (in module sphero_vem.registration.cropping) refine_crop() (in module sphero_vem.registration.cropping) refine_crop_multistart() (in module sphero_vem.registration.cropping) region_fill() (in module sphero_vem.segmentation.cellpose.utils) register_image_pair() (in module sphero_vem.registration.core) register_stack() (in module sphero_vem.registration.core) RegistrationConfig (class in sphero_vem.registration.core) repair_multiscales() (in module sphero_vem.utils.misc) resample_array() (in module sphero_vem.preprocessing) rough_crop_search() (in module sphero_vem.registration.cropping) S save() (sphero_vem.segmentation.np.core.NanoparticleSegmentation method) save_losses() (sphero_vem.segmentation.cellpose.finetuning.CellposeLogger method) save_n2v_config() (sphero_vem.denoising.DenoisingConfig method) save_regionprops() (in module sphero_vem.measure.pipeline) slice_from_bbox() (in module sphero_vem.utils.misc) sphero_vem.denoising module sphero_vem.io module sphero_vem.measure.distance module sphero_vem.measure.fractal module sphero_vem.measure.mesh module sphero_vem.measure.pipeline module sphero_vem.measure.sdf module sphero_vem.measure.voxel module sphero_vem.metrics module sphero_vem.preprocessing module sphero_vem.registration.core module sphero_vem.registration.cropping module sphero_vem.registration.transforms module sphero_vem.segmentation.cellpose.core module sphero_vem.segmentation.cellpose.evaluation module sphero_vem.segmentation.cellpose.finetuning module sphero_vem.segmentation.cellpose.utils module sphero_vem.segmentation.np.core module sphero_vem.segmentation.np.utils module sphero_vem.utils.accelerator module sphero_vem.utils.config module sphero_vem.utils.misc module stack_root (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) stack_to_zarr() (in module sphero_vem.io) stop() (sphero_vem.segmentation.cellpose.finetuning.CellposeLogger method) summary_fit (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) T temporary_zarr() (in module sphero_vem.utils.misc) timestamp() (in module sphero_vem.utils.misc) to_device() (in module sphero_vem.utils.accelerator) to_dict() (sphero_vem.utils.config.ProcessingStep method) to_host() (in module sphero_vem.utils.accelerator) to_json() (sphero_vem.utils.config.BaseConfig method) to_serializable() (in module sphero_vem.utils.config) train_n2v() (in module sphero_vem.denoising) TransformType (class in sphero_vem.registration.transforms) U update() (sphero_vem.denoising.DenoisingStats method) upsample_masks() (in module sphero_vem.segmentation.cellpose.utils) V volume_stack (sphero_vem.segmentation.np.core.NanoparticleSegmentation attribute) vprint() (in module sphero_vem.utils.misc) W weighted_std() (in module sphero_vem.utils.misc) write_image() (in module sphero_vem.io) write_zarr() (in module sphero_vem.io)