micro_dl module

Submodules

• micro_dl.cli module
  • Submodules
  • micro_dl.cli.dataset_pooling module
    • parse_args()
    • pool_dataset()
  • micro_dl.cli.inference_script module
    • parse_args()
    • run_inference()
  • micro_dl.cli.metrics_script module
    • compute_metrics()
    • parse_args()
  • micro_dl.cli.preprocess_script module
    • flat_field_correct()
    • generate_masks()
    • generate_zscore_table()
    • get_required_params()
    • parse_args()
    • pre_process()
    • resize_images()
    • save_config()
    • tile_images()
  • micro_dl.cli.train_script module
    • create_datasets()
    • create_network()
    • get_image_dir_format()
    • parse_args()
    • run_action()
  • Module contents
• micro_dl.inference module
  • Submodules
  • micro_dl.inference.evaluation_metrics module
    • MetricsEstimator
      • MetricsEstimator.assert_input()
      • MetricsEstimator.compute_metrics_row()
      • MetricsEstimator.estimate_xy_metrics()
      • MetricsEstimator.estimate_xyz_metrics()
      • MetricsEstimator.estimate_xz_metrics()
      • MetricsEstimator.estimate_yz_metrics()
      • MetricsEstimator.get_metrics_xy()
      • MetricsEstimator.get_metrics_xyz()
      • MetricsEstimator.get_metrics_xz()
      • MetricsEstimator.get_metrics_yz()
      • MetricsEstimator.mask_to_bool()
    • accuracy_metric()
    • binarize_array()
    • corr_metric()
    • dice_metric()
    • mae_metric()
    • mask_decorator()
    • mse_metric()
    • r2_metric()
    • ssim_metric()
  • micro_dl.inference.image_inference module
    • ImagePredictor
      • ImagePredictor.estimate_metrics()
      • ImagePredictor.get_mask()
      • ImagePredictor.predict_2d()
      • ImagePredictor.predict_3d()
      • ImagePredictor.run_prediction()
      • ImagePredictor.save_pred_image()
      • ImagePredictor.unzscore()
  • micro_dl.inference.model_inference module
    • load_model()
    • predict_large_image()
  • micro_dl.inference.stitch_predictions module
    • ImageStitcher
      • ImageStitcher.stitch_predictions()
  • Module contents
• micro_dl.input module
  • Submodules
  • micro_dl.input.dataset module
    • BaseDataSet
      • BaseDataSet.get_steps_per_epoch()
      • BaseDataSet.on_epoch_end()
    • apply_affine_transform()
    • transform_matrix_offset_center()
  • micro_dl.input.dataset_with_mask module
    • DataSetWithMask
  • micro_dl.input.inference_dataset module
    • InferenceDataSet
      • InferenceDataSet.adjust_slice_indices()
      • InferenceDataSet.get_iteration_meta()
  • micro_dl.input.training_table module
    • BaseTrainingTable
      • BaseTrainingTable.split_train_val_test()
      • BaseTrainingTable.train_test_split()
  • Module contents
• micro_dl.networks module
  • Submodules
    • micro_dl.networks.layers module
      • Submodules
      • micro_dl.networks.layers.interp_upsampling2D module
      • micro_dl.networks.layers.interp_upsampling3D module
      • Module contents
  • Submodules
  • micro_dl.networks.base_conv_net module
    • BaseConvNet
      • BaseConvNet.build_net()
  • micro_dl.networks.base_image_to_vector_net module
    • BaseImageToVectorNet
      • BaseImageToVectorNet.build_net()
  • micro_dl.networks.base_unet module
    • BaseUNet
      • BaseUNet.build_net()
  • micro_dl.networks.conv_blocks module
    • conv_block()
    • downsample_conv_block()
    • pad_channels()
    • residual_conv_block()
    • residual_downsample_conv_block()
    • skip_merge()
  • micro_dl.networks.image2D_to_vector_net module
    • Image2DToVectorNet
  • micro_dl.networks.image3D_to_vector_net module
    • Image3DToVectorNet
  • micro_dl.networks.unet2D module
    • UNet2D
  • micro_dl.networks.unet3D module
    • UNet3D
  • micro_dl.networks.unet_stack_2D module
    • UNetStackTo2D
      • UNetStackTo2D.build_net()
  • micro_dl.networks.unet_stack_stack module
    • UNetStackToStack
      • UNetStackToStack.build_net()
  • micro_dl.networks.vqnet module
    • VQVAE
      • VQVAE.build_net()
      • VQVAE.decoder_pass()
      • VQVAE.encoder_pass()
    • VectorQuantizer
      • VectorQuantizer.build()
      • VectorQuantizer.call()
      • VectorQuantizer.sample()
  • Module contents
• micro_dl.plotting module
  • Submodules
  • micro_dl.plotting.plot_utils module
    • convert_to_8bit()
    • save_center_slices()
    • save_mask_overlay()
    • save_plot()
    • save_predicted_images()
  • Module contents
• micro_dl.preprocessing module
  • Submodules
  • micro_dl.preprocessing.estimate_flat_field module
    • FlatFieldEstimator2D
      • FlatFieldEstimator2D.estimate_flat_field()
      • FlatFieldEstimator2D.get_flat_field_dir()
      • FlatFieldEstimator2D.get_flatfield()
      • FlatFieldEstimator2D.sample_block_medians()
  • micro_dl.preprocessing.generate_masks module
    • MaskProcessor
      • MaskProcessor.generate_masks()
      • MaskProcessor.get_channel_thr_df()
      • MaskProcessor.get_mask_channel()
      • MaskProcessor.get_mask_dir()
  • micro_dl.preprocessing.resize_images module
    • ImageResizer
      • ImageResizer.get_resize_dir()
      • ImageResizer.resize_frames()
      • ImageResizer.resize_volumes()
  • micro_dl.preprocessing.tile_3d module
    • ImageTilerUniform3D
  • micro_dl.preprocessing.tile_nonuniform_images module
    • ImageTilerNonUniform
      • ImageTilerNonUniform.tile_first_channel()
      • ImageTilerNonUniform.tile_mask_stack()
      • ImageTilerNonUniform.tile_remaining_channels()
      • ImageTilerNonUniform.tile_stack()
  • micro_dl.preprocessing.tile_uniform_images module
    • ImageTilerUniform
      • ImageTilerUniform.get_crop_tile_args()
      • ImageTilerUniform.get_tile_dir()
      • ImageTilerUniform.tile_mask_stack()
      • ImageTilerUniform.tile_stack()
  • Module contents
• micro_dl.train module
  • Submodules
  • micro_dl.train.learning_rates module
    • CyclicLearning
      • CyclicLearning.clr()
      • CyclicLearning.on_batch_end()
      • CyclicLearning.on_epoch_end()
      • CyclicLearning.on_train_begin()
  • micro_dl.train.losses module
    • binary_crossentropy_loss()
    • dice_coef_loss()
    • dssim_loss()
    • kl_divergence_loss()
    • latent_loss()
    • mae_loss()
    • masked_loss()
    • ms_ssim_loss()
    • mse_loss()
  • micro_dl.train.lr_finder module
    • LRFinder
      • LRFinder.on_batch_end()
      • LRFinder.on_train_begin()
      • LRFinder.on_train_end()
  • micro_dl.train.metrics module
    • binary_accuracy()
    • coeff_determination()
    • dice_coef()
    • flip_dimensions()
    • mask_accuracy()
    • mask_coeff_determination()
    • ms_ssim()
    • pearson_corr()
    • ssim()
  • micro_dl.train.trainer module
    • BaseKerasTrainer
      • BaseKerasTrainer.train()
  • Module contents
• micro_dl.utils module
  • Submodules
  • micro_dl.utils.aux_utils module
    • adjust_slice_margins()
    • convert_channel_names_to_ids()
    • get_channel_axis()
    • get_channels()
    • get_im_name()
    • get_meta_idx()
    • get_row_idx()
    • get_sms_im_name()
    • get_sorted_names()
    • get_sub_meta()
    • import_object()
    • init_logger()
    • make_dataframe()
    • parse_idx_from_name()
    • parse_sms_name()
    • read_config()
    • read_json()
    • read_meta()
    • save_tile_meta()
    • sort_meta_by_channel()
    • validate_config()
    • validate_indices()
    • validate_metadata_indices()
    • write_json()
  • micro_dl.utils.image_utils module
    • apply_flat_field_correction()
    • center_crop_to_shape()
    • crop2base()
    • fit_polynomial_surface_2D()
    • get_flat_field_path()
    • grid_sample_pixel_values()
    • im_adjust()
    • im_bit_convert()
    • preprocess_image()
    • preprocess_imstack()
    • read_image()
    • read_image_from_row()
    • read_imstack()
    • read_imstack_from_meta()
    • rescale_image()
    • rescale_nd_image()
    • resize_image()
    • resize_mask()
  • micro_dl.utils.io_utils module
    • DefaultZarr
      • DefaultZarr.create_position()
      • DefaultZarr.init_hierarchy()
    • ReaderBase
      • ReaderBase.get_array()
      • ReaderBase.get_image()
      • ReaderBase.get_num_positions()
      • ReaderBase.get_zarr()
      • ReaderBase.shape
    • WriterBase
      • WriterBase.create_channel_dict()
      • WriterBase.create_column()
      • WriterBase.create_position()
      • WriterBase.create_row()
      • WriterBase.get_zarr()
      • WriterBase.init_array()
      • WriterBase.init_hierarchy()
      • WriterBase.open_position()
      • WriterBase.set_channel_attributes()
      • WriterBase.set_root()
      • WriterBase.set_store()
      • WriterBase.set_verbosity()
      • WriterBase.write()
    • ZarrReader
      • ZarrReader.get_array()
      • ZarrReader.get_image()
      • ZarrReader.get_image_plane_metadata()
      • ZarrReader.get_num_positions()
      • ZarrReader.get_zarr()
    • ZarrWriter
      • ZarrWriter.create_zarr_root()
      • ZarrWriter.current_group_name
      • ZarrWriter.current_position
      • ZarrWriter.init_array()
      • ZarrWriter.store
      • ZarrWriter.write()
  • micro_dl.utils.masks module
    • create_otsu_mask()
    • create_unimodal_mask()
    • get_unet_border_weight_map()
    • get_unimodal_threshold()
  • micro_dl.utils.meta_utils module
    • compute_zscore_params()
    • frames_meta_from_filenames()
    • frames_meta_from_zarr()
    • frames_meta_generator()
    • ints_meta_generator()
    • mask_meta_generator()
  • micro_dl.utils.mp_utils module
    • create_save_mask()
    • crop_at_indices_save()
    • get_im_stats()
    • get_mask_meta_row()
    • mp_create_save_mask()
    • mp_crop_save()
    • mp_get_im_stats()
    • mp_rescale_vol()
    • mp_resize_save()
    • mp_sample_im_pixels()
    • mp_tile_save()
    • mp_wrapper()
    • rescale_vol_and_save()
    • resize_and_save()
    • sample_im_pixels()
    • tile_and_save()
  • micro_dl.utils.network_utils module
    • create_activation_layer()
    • get_keras_layer()
    • get_layer_shape()
  • micro_dl.utils.normalize module
    • hist_adapteq_2D()
    • hist_clipping()
    • unzscore()
    • zscore()
  • micro_dl.utils.preprocess_utils module
    • get_preprocess_config()
    • validate_mask_meta()
  • micro_dl.utils.tile_utils module
    • crop_at_indices()
    • tile_image()
    • write_meta()
    • write_tile()
  • micro_dl.utils.train_utils module
    • check_gpu_availability()
    • get_loss()
    • get_metrics()
    • select_gpu()
    • set_keras_session()
  • Module contents

Module contents

DL package for microscopy