microDL
Contents:
micro_dl
microDL
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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O
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P
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R
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S
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T
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U
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V
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W
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Z
A
accuracy_metric() (in module micro_dl.inference.evaluation_metrics)
adjust_slice_indices() (micro_dl.input.inference_dataset.InferenceDataSet method)
adjust_slice_margins() (in module micro_dl.utils.aux_utils)
apply_affine_transform() (in module micro_dl.input.dataset)
apply_flat_field_correction() (in module micro_dl.utils.image_utils)
assert_input() (micro_dl.inference.evaluation_metrics.MetricsEstimator static method)
B
BaseConvNet (class in micro_dl.networks.base_conv_net)
BaseDataSet (class in micro_dl.input.dataset)
BaseImageToVectorNet (class in micro_dl.networks.base_image_to_vector_net)
BaseKerasTrainer (class in micro_dl.train.trainer)
BaseTrainingTable (class in micro_dl.input.training_table)
BaseUNet (class in micro_dl.networks.base_unet)
binarize_array() (in module micro_dl.inference.evaluation_metrics)
binary_accuracy() (in module micro_dl.train.metrics)
binary_crossentropy_loss() (in module micro_dl.train.losses)
build() (micro_dl.networks.layers.interp_upsampling2D.InterpUpSampling2D method)
(micro_dl.networks.layers.interp_upsampling3D.InterpUpSampling3D method)
(micro_dl.networks.vqnet.VectorQuantizer method)
build_net() (micro_dl.networks.base_conv_net.BaseConvNet method)
(micro_dl.networks.base_image_to_vector_net.BaseImageToVectorNet method)
(micro_dl.networks.base_unet.BaseUNet method)
(micro_dl.networks.unet_stack_2D.UNetStackTo2D method)
(micro_dl.networks.unet_stack_stack.UNetStackToStack method)
(micro_dl.networks.vqnet.VQVAE method)
C
call() (micro_dl.networks.layers.interp_upsampling2D.InterpUpSampling2D method)
(micro_dl.networks.layers.interp_upsampling3D.InterpUpSampling3D method)
(micro_dl.networks.vqnet.VectorQuantizer method)
center_crop_to_shape() (in module micro_dl.utils.image_utils)
check_gpu_availability() (in module micro_dl.utils.train_utils)
clr() (micro_dl.train.learning_rates.CyclicLearning method)
coeff_determination() (in module micro_dl.train.metrics)
compute_metrics() (in module micro_dl.cli.metrics_script)
compute_metrics_row() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
compute_output_shape() (micro_dl.networks.layers.interp_upsampling2D.InterpUpSampling2D method)
(micro_dl.networks.layers.interp_upsampling3D.InterpUpSampling3D method)
compute_zscore_params() (in module micro_dl.utils.meta_utils)
conv_block() (in module micro_dl.networks.conv_blocks)
convert_channel_names_to_ids() (in module micro_dl.utils.aux_utils)
convert_to_8bit() (in module micro_dl.plotting.plot_utils)
corr_metric() (in module micro_dl.inference.evaluation_metrics)
create_activation_layer() (in module micro_dl.utils.network_utils)
create_channel_dict() (micro_dl.utils.io_utils.WriterBase method)
create_column() (micro_dl.utils.io_utils.WriterBase method)
create_datasets() (in module micro_dl.cli.train_script)
create_network() (in module micro_dl.cli.train_script)
create_otsu_mask() (in module micro_dl.utils.masks)
create_position() (micro_dl.utils.io_utils.DefaultZarr method)
(micro_dl.utils.io_utils.WriterBase method)
create_row() (micro_dl.utils.io_utils.WriterBase method)
create_save_mask() (in module micro_dl.utils.mp_utils)
create_unimodal_mask() (in module micro_dl.utils.masks)
create_zarr_root() (micro_dl.utils.io_utils.ZarrWriter method)
crop2base() (in module micro_dl.utils.image_utils)
crop_at_indices() (in module micro_dl.utils.tile_utils)
crop_at_indices_save() (in module micro_dl.utils.mp_utils)
current_group_name (micro_dl.utils.io_utils.ZarrWriter attribute)
current_position (micro_dl.utils.io_utils.ZarrWriter attribute)
CyclicLearning (class in micro_dl.train.learning_rates)
D
DataSetWithMask (class in micro_dl.input.dataset_with_mask)
decoder_pass() (micro_dl.networks.vqnet.VQVAE method)
DefaultZarr (class in micro_dl.utils.io_utils)
dice_coef() (in module micro_dl.train.metrics)
dice_coef_loss() (in module micro_dl.train.losses)
dice_metric() (in module micro_dl.inference.evaluation_metrics)
downsample_conv_block() (in module micro_dl.networks.conv_blocks)
dssim_loss() (in module micro_dl.train.losses)
E
encoder_pass() (micro_dl.networks.vqnet.VQVAE method)
estimate_flat_field() (micro_dl.preprocessing.estimate_flat_field.FlatFieldEstimator2D method)
estimate_metrics() (micro_dl.inference.image_inference.ImagePredictor method)
estimate_xy_metrics() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
estimate_xyz_metrics() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
estimate_xz_metrics() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
estimate_yz_metrics() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
F
fit_polynomial_surface_2D() (in module micro_dl.utils.image_utils)
flat_field_correct() (in module micro_dl.cli.preprocess_script)
FlatFieldEstimator2D (class in micro_dl.preprocessing.estimate_flat_field)
flip_dimensions() (in module micro_dl.train.metrics)
frames_meta_from_filenames() (in module micro_dl.utils.meta_utils)
frames_meta_from_zarr() (in module micro_dl.utils.meta_utils)
frames_meta_generator() (in module micro_dl.utils.meta_utils)
G
generate_masks() (in module micro_dl.cli.preprocess_script)
(micro_dl.preprocessing.generate_masks.MaskProcessor method)
generate_zscore_table() (in module micro_dl.cli.preprocess_script)
get_array() (micro_dl.utils.io_utils.ReaderBase method)
(micro_dl.utils.io_utils.ZarrReader method)
get_channel_axis() (in module micro_dl.utils.aux_utils)
get_channel_thr_df() (micro_dl.preprocessing.generate_masks.MaskProcessor method)
get_channels() (in module micro_dl.utils.aux_utils)
get_config() (micro_dl.networks.layers.interp_upsampling2D.InterpUpSampling2D method)
(micro_dl.networks.layers.interp_upsampling3D.InterpUpSampling3D method)
get_crop_tile_args() (micro_dl.preprocessing.tile_uniform_images.ImageTilerUniform method)
get_flat_field_dir() (micro_dl.preprocessing.estimate_flat_field.FlatFieldEstimator2D method)
get_flat_field_path() (in module micro_dl.utils.image_utils)
get_flatfield() (micro_dl.preprocessing.estimate_flat_field.FlatFieldEstimator2D method)
get_im_name() (in module micro_dl.utils.aux_utils)
get_im_stats() (in module micro_dl.utils.mp_utils)
get_image() (micro_dl.utils.io_utils.ReaderBase method)
(micro_dl.utils.io_utils.ZarrReader method)
get_image_dir_format() (in module micro_dl.cli.train_script)
get_image_plane_metadata() (micro_dl.utils.io_utils.ZarrReader method)
get_iteration_meta() (micro_dl.input.inference_dataset.InferenceDataSet method)
get_keras_layer() (in module micro_dl.utils.network_utils)
get_layer_shape() (in module micro_dl.utils.network_utils)
get_loss() (in module micro_dl.utils.train_utils)
get_mask() (micro_dl.inference.image_inference.ImagePredictor method)
get_mask_channel() (micro_dl.preprocessing.generate_masks.MaskProcessor method)
get_mask_dir() (micro_dl.preprocessing.generate_masks.MaskProcessor method)
get_mask_meta_row() (in module micro_dl.utils.mp_utils)
get_meta_idx() (in module micro_dl.utils.aux_utils)
get_metrics() (in module micro_dl.utils.train_utils)
get_metrics_xy() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
get_metrics_xyz() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
get_metrics_xz() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
get_metrics_yz() (micro_dl.inference.evaluation_metrics.MetricsEstimator method)
get_num_positions() (micro_dl.utils.io_utils.ReaderBase method)
(micro_dl.utils.io_utils.ZarrReader method)
get_preprocess_config() (in module micro_dl.utils.preprocess_utils)
get_required_params() (in module micro_dl.cli.preprocess_script)
get_resize_dir() (micro_dl.preprocessing.resize_images.ImageResizer method)
get_row_idx() (in module micro_dl.utils.aux_utils)
get_sms_im_name() (in module micro_dl.utils.aux_utils)
get_sorted_names() (in module micro_dl.utils.aux_utils)
get_steps_per_epoch() (micro_dl.input.dataset.BaseDataSet method)
get_sub_meta() (in module micro_dl.utils.aux_utils)
get_tile_dir() (micro_dl.preprocessing.tile_uniform_images.ImageTilerUniform method)
get_unet_border_weight_map() (in module micro_dl.utils.masks)
get_unimodal_threshold() (in module micro_dl.utils.masks)
get_zarr() (micro_dl.utils.io_utils.ReaderBase method)
(micro_dl.utils.io_utils.WriterBase method)
(micro_dl.utils.io_utils.ZarrReader method)
grid_sample_pixel_values() (in module micro_dl.utils.image_utils)
H
hist_adapteq_2D() (in module micro_dl.utils.normalize)
hist_clipping() (in module micro_dl.utils.normalize)
I
im_adjust() (in module micro_dl.utils.image_utils)
im_bit_convert() (in module micro_dl.utils.image_utils)
Image2DToVectorNet (class in micro_dl.networks.image2D_to_vector_net)
Image3DToVectorNet (class in micro_dl.networks.image3D_to_vector_net)
ImagePredictor (class in micro_dl.inference.image_inference)
ImageResizer (class in micro_dl.preprocessing.resize_images)
ImageStitcher (class in micro_dl.inference.stitch_predictions)
ImageTilerNonUniform (class in micro_dl.preprocessing.tile_nonuniform_images)
ImageTilerUniform (class in micro_dl.preprocessing.tile_uniform_images)
ImageTilerUniform3D (class in micro_dl.preprocessing.tile_3d)
import_object() (in module micro_dl.utils.aux_utils)
InferenceDataSet (class in micro_dl.input.inference_dataset)
init_array() (micro_dl.utils.io_utils.WriterBase method)
(micro_dl.utils.io_utils.ZarrWriter method)
init_hierarchy() (micro_dl.utils.io_utils.DefaultZarr method)
(micro_dl.utils.io_utils.WriterBase method)
init_logger() (in module micro_dl.utils.aux_utils)
InterpUpSampling2D (class in micro_dl.networks.layers.interp_upsampling2D)
InterpUpSampling3D (class in micro_dl.networks.layers.interp_upsampling3D)
ints_meta_generator() (in module micro_dl.utils.meta_utils)
K
kl_divergence_loss() (in module micro_dl.train.losses)
L
latent_loss() (in module micro_dl.train.losses)
load_model() (in module micro_dl.inference.model_inference)
LRFinder (class in micro_dl.train.lr_finder)
M
mae_loss() (in module micro_dl.train.losses)
mae_metric() (in module micro_dl.inference.evaluation_metrics)
make_dataframe() (in module micro_dl.utils.aux_utils)
mask_accuracy() (in module micro_dl.train.metrics)
mask_coeff_determination() (in module micro_dl.train.metrics)
mask_decorator() (in module micro_dl.inference.evaluation_metrics)
mask_meta_generator() (in module micro_dl.utils.meta_utils)
mask_to_bool() (micro_dl.inference.evaluation_metrics.MetricsEstimator static method)
masked_loss() (in module micro_dl.train.losses)
MaskProcessor (class in micro_dl.preprocessing.generate_masks)
MetricsEstimator (class in micro_dl.inference.evaluation_metrics)
micro_dl
module
micro_dl.cli
module
micro_dl.cli.dataset_pooling
module
micro_dl.cli.inference_script
module
micro_dl.cli.metrics_script
module
micro_dl.cli.preprocess_script
module
micro_dl.cli.train_script
module
micro_dl.inference
module
micro_dl.inference.evaluation_metrics
module
micro_dl.inference.image_inference
module
micro_dl.inference.model_inference
module
micro_dl.inference.stitch_predictions
module
micro_dl.input
module
micro_dl.input.dataset
module
micro_dl.input.dataset_with_mask
module
micro_dl.input.inference_dataset
module
micro_dl.input.training_table
module
micro_dl.networks
module
micro_dl.networks.base_conv_net
module
micro_dl.networks.base_image_to_vector_net
module
micro_dl.networks.base_unet
module
micro_dl.networks.conv_blocks
module
micro_dl.networks.image2D_to_vector_net
module
micro_dl.networks.image3D_to_vector_net
module
micro_dl.networks.layers
module
micro_dl.networks.layers.interp_upsampling2D
module
micro_dl.networks.layers.interp_upsampling3D
module
micro_dl.networks.unet2D
module
micro_dl.networks.unet3D
module
micro_dl.networks.unet_stack_2D
module
micro_dl.networks.unet_stack_stack
module
micro_dl.networks.vqnet
module
micro_dl.plotting
module
micro_dl.plotting.plot_utils
module
micro_dl.preprocessing
module
micro_dl.preprocessing.estimate_flat_field
module
micro_dl.preprocessing.generate_masks
module
micro_dl.preprocessing.resize_images
module
micro_dl.preprocessing.tile_3d
module
micro_dl.preprocessing.tile_nonuniform_images
module
micro_dl.preprocessing.tile_uniform_images
module
micro_dl.train
module
micro_dl.train.learning_rates
module
micro_dl.train.losses
module
micro_dl.train.lr_finder
module
micro_dl.train.metrics
module
micro_dl.train.trainer
module
micro_dl.utils
module
micro_dl.utils.aux_utils
module
micro_dl.utils.image_utils
module
micro_dl.utils.io_utils
module
micro_dl.utils.masks
module
micro_dl.utils.meta_utils
module
micro_dl.utils.mp_utils
module
micro_dl.utils.network_utils
module
micro_dl.utils.normalize
module
micro_dl.utils.preprocess_utils
module
micro_dl.utils.tile_utils
module
micro_dl.utils.train_utils
module
module
micro_dl
micro_dl.cli
micro_dl.cli.dataset_pooling
micro_dl.cli.inference_script
micro_dl.cli.metrics_script
micro_dl.cli.preprocess_script
micro_dl.cli.train_script
micro_dl.inference
micro_dl.inference.evaluation_metrics
micro_dl.inference.image_inference
micro_dl.inference.model_inference
micro_dl.inference.stitch_predictions
micro_dl.input
micro_dl.input.dataset
micro_dl.input.dataset_with_mask
micro_dl.input.inference_dataset
micro_dl.input.training_table
micro_dl.networks
micro_dl.networks.base_conv_net
micro_dl.networks.base_image_to_vector_net
micro_dl.networks.base_unet
micro_dl.networks.conv_blocks
micro_dl.networks.image2D_to_vector_net
micro_dl.networks.image3D_to_vector_net
micro_dl.networks.layers
micro_dl.networks.layers.interp_upsampling2D
micro_dl.networks.layers.interp_upsampling3D
micro_dl.networks.unet2D
micro_dl.networks.unet3D
micro_dl.networks.unet_stack_2D
micro_dl.networks.unet_stack_stack
micro_dl.networks.vqnet
micro_dl.plotting
micro_dl.plotting.plot_utils
micro_dl.preprocessing
micro_dl.preprocessing.estimate_flat_field
micro_dl.preprocessing.generate_masks
micro_dl.preprocessing.resize_images
micro_dl.preprocessing.tile_3d
micro_dl.preprocessing.tile_nonuniform_images
micro_dl.preprocessing.tile_uniform_images
micro_dl.train
micro_dl.train.learning_rates
micro_dl.train.losses
micro_dl.train.lr_finder
micro_dl.train.metrics
micro_dl.train.trainer
micro_dl.utils
micro_dl.utils.aux_utils
micro_dl.utils.image_utils
micro_dl.utils.io_utils
micro_dl.utils.masks
micro_dl.utils.meta_utils
micro_dl.utils.mp_utils
micro_dl.utils.network_utils
micro_dl.utils.normalize
micro_dl.utils.preprocess_utils
micro_dl.utils.tile_utils
micro_dl.utils.train_utils
mp_create_save_mask() (in module micro_dl.utils.mp_utils)
mp_crop_save() (in module micro_dl.utils.mp_utils)
mp_get_im_stats() (in module micro_dl.utils.mp_utils)
mp_rescale_vol() (in module micro_dl.utils.mp_utils)
mp_resize_save() (in module micro_dl.utils.mp_utils)
mp_sample_im_pixels() (in module micro_dl.utils.mp_utils)
mp_tile_save() (in module micro_dl.utils.mp_utils)
mp_wrapper() (in module micro_dl.utils.mp_utils)
ms_ssim() (in module micro_dl.train.metrics)
ms_ssim_loss() (in module micro_dl.train.losses)
mse_loss() (in module micro_dl.train.losses)
mse_metric() (in module micro_dl.inference.evaluation_metrics)
O
on_batch_end() (micro_dl.train.learning_rates.CyclicLearning method)
(micro_dl.train.lr_finder.LRFinder method)
on_epoch_end() (micro_dl.input.dataset.BaseDataSet method)
(micro_dl.train.learning_rates.CyclicLearning method)
on_train_begin() (micro_dl.train.learning_rates.CyclicLearning method)
(micro_dl.train.lr_finder.LRFinder method)
on_train_end() (micro_dl.train.lr_finder.LRFinder method)
open_position() (micro_dl.utils.io_utils.WriterBase method)
P
pad_channels() (in module micro_dl.networks.conv_blocks)
parse_args() (in module micro_dl.cli.dataset_pooling)
(in module micro_dl.cli.inference_script)
(in module micro_dl.cli.metrics_script)
(in module micro_dl.cli.preprocess_script)
(in module micro_dl.cli.train_script)
parse_idx_from_name() (in module micro_dl.utils.aux_utils)
parse_sms_name() (in module micro_dl.utils.aux_utils)
pearson_corr() (in module micro_dl.train.metrics)
pool_dataset() (in module micro_dl.cli.dataset_pooling)
pre_process() (in module micro_dl.cli.preprocess_script)
predict_2d() (micro_dl.inference.image_inference.ImagePredictor method)
predict_3d() (micro_dl.inference.image_inference.ImagePredictor method)
predict_large_image() (in module micro_dl.inference.model_inference)
preprocess_image() (in module micro_dl.utils.image_utils)
preprocess_imstack() (in module micro_dl.utils.image_utils)
R
r2_metric() (in module micro_dl.inference.evaluation_metrics)
read_config() (in module micro_dl.utils.aux_utils)
read_image() (in module micro_dl.utils.image_utils)
read_image_from_row() (in module micro_dl.utils.image_utils)
read_imstack() (in module micro_dl.utils.image_utils)
read_imstack_from_meta() (in module micro_dl.utils.image_utils)
read_json() (in module micro_dl.utils.aux_utils)
read_meta() (in module micro_dl.utils.aux_utils)
ReaderBase (class in micro_dl.utils.io_utils)
rescale_image() (in module micro_dl.utils.image_utils)
rescale_nd_image() (in module micro_dl.utils.image_utils)
rescale_vol_and_save() (in module micro_dl.utils.mp_utils)
residual_conv_block() (in module micro_dl.networks.conv_blocks)
residual_downsample_conv_block() (in module micro_dl.networks.conv_blocks)
resize_and_save() (in module micro_dl.utils.mp_utils)
resize_frames() (micro_dl.preprocessing.resize_images.ImageResizer method)
resize_image() (in module micro_dl.utils.image_utils)
resize_images() (in module micro_dl.cli.preprocess_script)
resize_mask() (in module micro_dl.utils.image_utils)
resize_volumes() (micro_dl.preprocessing.resize_images.ImageResizer method)
run_action() (in module micro_dl.cli.train_script)
run_inference() (in module micro_dl.cli.inference_script)
run_prediction() (micro_dl.inference.image_inference.ImagePredictor method)
S
sample() (micro_dl.networks.vqnet.VectorQuantizer method)
sample_block_medians() (micro_dl.preprocessing.estimate_flat_field.FlatFieldEstimator2D method)
sample_im_pixels() (in module micro_dl.utils.mp_utils)
save_center_slices() (in module micro_dl.plotting.plot_utils)
save_config() (in module micro_dl.cli.preprocess_script)
save_mask_overlay() (in module micro_dl.plotting.plot_utils)
save_plot() (in module micro_dl.plotting.plot_utils)
save_pred_image() (micro_dl.inference.image_inference.ImagePredictor method)
save_predicted_images() (in module micro_dl.plotting.plot_utils)
save_tile_meta() (in module micro_dl.utils.aux_utils)
select_gpu() (in module micro_dl.utils.train_utils)
set_channel_attributes() (micro_dl.utils.io_utils.WriterBase method)
set_keras_session() (in module micro_dl.utils.train_utils)
set_root() (micro_dl.utils.io_utils.WriterBase method)
set_store() (micro_dl.utils.io_utils.WriterBase method)
set_verbosity() (micro_dl.utils.io_utils.WriterBase method)
shape (micro_dl.utils.io_utils.ReaderBase property)
skip_merge() (in module micro_dl.networks.conv_blocks)
sort_meta_by_channel() (in module micro_dl.utils.aux_utils)
split_train_val_test() (micro_dl.input.training_table.BaseTrainingTable static method)
ssim() (in module micro_dl.train.metrics)
ssim_metric() (in module micro_dl.inference.evaluation_metrics)
stitch_predictions() (micro_dl.inference.stitch_predictions.ImageStitcher method)
store (micro_dl.utils.io_utils.ZarrWriter attribute)
T
tile_and_save() (in module micro_dl.utils.mp_utils)
tile_first_channel() (micro_dl.preprocessing.tile_nonuniform_images.ImageTilerNonUniform method)
tile_image() (in module micro_dl.utils.tile_utils)
tile_images() (in module micro_dl.cli.preprocess_script)
tile_mask_stack() (micro_dl.preprocessing.tile_nonuniform_images.ImageTilerNonUniform method)
(micro_dl.preprocessing.tile_uniform_images.ImageTilerUniform method)
tile_remaining_channels() (micro_dl.preprocessing.tile_nonuniform_images.ImageTilerNonUniform method)
tile_stack() (micro_dl.preprocessing.tile_nonuniform_images.ImageTilerNonUniform method)
(micro_dl.preprocessing.tile_uniform_images.ImageTilerUniform method)
train() (micro_dl.train.trainer.BaseKerasTrainer method)
train_test_split() (micro_dl.input.training_table.BaseTrainingTable method)
transform_matrix_offset_center() (in module micro_dl.input.dataset)
U
UNet2D (class in micro_dl.networks.unet2D)
UNet3D (class in micro_dl.networks.unet3D)
UNetStackTo2D (class in micro_dl.networks.unet_stack_2D)
UNetStackToStack (class in micro_dl.networks.unet_stack_stack)
unzscore() (in module micro_dl.utils.normalize)
(micro_dl.inference.image_inference.ImagePredictor method)
V
validate_config() (in module micro_dl.utils.aux_utils)
validate_indices() (in module micro_dl.utils.aux_utils)
validate_mask_meta() (in module micro_dl.utils.preprocess_utils)
validate_metadata_indices() (in module micro_dl.utils.aux_utils)
VectorQuantizer (class in micro_dl.networks.vqnet)
VQVAE (class in micro_dl.networks.vqnet)
W
write() (micro_dl.utils.io_utils.WriterBase method)
(micro_dl.utils.io_utils.ZarrWriter method)
write_json() (in module micro_dl.utils.aux_utils)
write_meta() (in module micro_dl.utils.tile_utils)
write_tile() (in module micro_dl.utils.tile_utils)
WriterBase (class in micro_dl.utils.io_utils)
Z
ZarrReader (class in micro_dl.utils.io_utils)
ZarrWriter (class in micro_dl.utils.io_utils)
zscore() (in module micro_dl.utils.normalize)