.gitignore
CODE_OF_CONDUCT.md
LICENSE.md
README.md
main.py
pyproject.toml
setup.py
biapy/__init__.py
biapy/_biapy.py
biapy.egg-info/PKG-INFO
biapy.egg-info/SOURCES.txt
biapy.egg-info/dependency_links.txt
biapy.egg-info/requires.txt
biapy.egg-info/top_level.txt
biapy/config/__init__.py
biapy/config/config.py
biapy/data/__init__.py
biapy/data/data_2D_manipulation.py
biapy/data/data_3D_manipulation.py
biapy/data/pre_processing.py
biapy/data/generators/__init__.py
biapy/data/generators/augmentors.py
biapy/data/generators/pair_base_data_generator.py
biapy/data/generators/pair_data_2D_generator.py
biapy/data/generators/pair_data_3D_generator.py
biapy/data/generators/single_base_data_generator.py
biapy/data/generators/single_data_2D_generator.py
biapy/data/generators/single_data_3D_generator.py
biapy/data/generators/test_pair_data_generators.py
biapy/data/generators/test_single_data_generator.py
biapy/data/post_processing/__init__.py
biapy/data/post_processing/post_processing.py
biapy/data/post_processing/smooth_tiled_predictions.py
biapy/engine/__init__.py
biapy/engine/base_workflow.py
biapy/engine/check_configuration.py
biapy/engine/classification.py
biapy/engine/denoising.py
biapy/engine/detection.py
biapy/engine/instance_seg.py
biapy/engine/metrics.py
biapy/engine/self_supervised.py
biapy/engine/semantic_seg.py
biapy/engine/super_resolution.py
biapy/engine/train_engine.py
biapy/engine/schedulers/warmup_cosine_decay.py
biapy/models/__init__.py
biapy/models/attention_unet.py
biapy/models/blocks.py
biapy/models/dfcan.py
biapy/models/edsr.py
biapy/models/efficientnet.py
biapy/models/mae.py
biapy/models/multiresunet.py
biapy/models/rcan.py
biapy/models/resunet++.py
biapy/models/resunet.py
biapy/models/seunet.py
biapy/models/simple_cnn.py
biapy/models/tr_layers.py
biapy/models/unet.py
biapy/models/unetr.py
biapy/models/vit.py
biapy/models/wdsr.py
biapy/utils/callbacks.py
biapy/utils/matching.py
biapy/utils/misc.py
biapy/utils/util.py
biapy/utils/env/Dockerfile
biapy/utils/env/Dockerfile_CUDA10.2
biapy/utils/env/create_docker_image.sh
biapy/utils/scripts/calculate_detection_metrics.py
biapy/utils/scripts/calculate_metrics_3D.py
biapy/utils/scripts/create_probability_csv.py
biapy/utils/scripts/crop_2D_dataset.py
biapy/utils/scripts/crop_3D_dataset.py
biapy/utils/scripts/crop_and_discard_3D_dataset.py
biapy/utils/scripts/detection_plots.py
biapy/utils/scripts/detection_probs_to_points.py
biapy/utils/scripts/fill_holes_in_seg_masks.py
biapy/utils/scripts/filter_close_points.py
biapy/utils/scripts/from_class_csv_to_folders.py
biapy/utils/scripts/h5_to_tif.py
biapy/utils/scripts/h5_to_zarr.py
biapy/utils/scripts/merge_dataset_channels.py
biapy/utils/scripts/order_axes.py
biapy/utils/scripts/tif_to_h5.py
img/BiaPy-Euro-BioImaging-youtube.png
img/BiaPy-workflow-readme.svg
img/BiaPy_GUI_main_page.png
img/BiaPy_presentation_and_demo_at_RTmfm.jpg
img/MitoEM_teaser_cable_length_split.png
img/biapy_logo.png
img/complex_MOAS.png
img/cyst_instance_prediction.gif
img/cyst_sample.gif
img/domain_EM.jpg
img/halo_instances.png
img/unet_attn_stable.png
img/wound_diagram_VQVAE.png
notebooks/BiaPy_Inference.ipynb
notebooks/classification/BiaPy_2D_Classification.ipynb
notebooks/classification/BiaPy_2D_Classification_Butterfly.ipynb
notebooks/classification/BiaPy_3D_Classification.ipynb
notebooks/denoising/BiaPy_2D_Denoising.ipynb
notebooks/denoising/BiaPy_3D_Denoising.ipynb
notebooks/detection/BiaPy_2D_Detection.ipynb
notebooks/detection/BiaPy_3D_Detection.ipynb
notebooks/instance_segmentation/BiaPy_2D_Instance_Segmentation.ipynb
notebooks/instance_segmentation/BiaPy_3D_Instance_Segmentation.ipynb
notebooks/self-supervised/BiaPy_2D_Self_Supervision.ipynb
notebooks/self-supervised/BiaPy_3D_Self_Supervision.ipynb
notebooks/semantic_segmentation/BiaPy_2D_Semantic_Segmentation.ipynb
notebooks/semantic_segmentation/BiaPy_3D_Semantic_Segmentation.ipynb
notebooks/super-resolution/BiaPy_2D_Super_Resolution.ipynb
notebooks/super-resolution/BiaPy_3D_Super_Resolution.ipynb
templates/classification/2d_classification.yaml
templates/classification/2d_classification_rgb.yaml
templates/classification/3d_classification.yaml
templates/denoising/2d_denoising.yaml
templates/denoising/3d_denoising.yaml
templates/detection/2d_detection.yaml
templates/detection/3d_detection.yaml
templates/instance_segmentation/2d_instance_segmentation.yaml
templates/instance_segmentation/3d_instance_segmentation.yaml
templates/instance_segmentation/CartoCell_paper/CartoCell - Inference workflow (Phase 5).ipynb
templates/instance_segmentation/CartoCell_paper/CartoCell - Training workflow (Phase 2).ipynb
templates/instance_segmentation/CartoCell_paper/cartocell_inference.yaml
templates/instance_segmentation/CartoCell_paper/cartocell_training.yaml
templates/instance_segmentation/CartoCell_paper/model_weights_cartocell.h5
templates/instance_segmentation/MitoEM_paper/mitoem.yaml
templates/self-supervised/2d_self-supervised.yaml
templates/self-supervised/3d_self-supervised.yaml
templates/semantic_segmentation/2d_semantic_segmentation.yaml
templates/semantic_segmentation/3d_semantic_segmentation.yaml
templates/semantic_segmentation/stable_paper/semantic_segmentation_workflow.ipynb
templates/sota_implementations/Casser_workflow.ipynb
templates/sota_implementations/Cheng_2D_workflow.ipynb
templates/sota_implementations/Cheng_3D_workflow.ipynb
templates/sota_implementations/Oztel_workflow.ipynb
templates/sota_implementations/Xiao_workflow.ipynb
templates/super-resolution/2d_super-resolution.yaml
templates/super-resolution/2d_super-resolution_rgb.yaml
templates/super-resolution/3d_super-resolution.yaml