.gitignore
.readthedocs.yaml
LICENSE
MANIFEST.in
README.rst
environment_cli.yml
environment_gui.yml
pyproject.toml
requirements_gui_pyqt5.txt
requirements_gui_pyqt6.txt
.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/enhanchement_request.yml
.github/ISSUE_TEMPLATE/feature_request.yml
.github/ISSUE_TEMPLATE/informal-request.yml
.github/workflows/build-macos_pyqt5.yml
.github/workflows/build-macos_pyqt6.yml
.github/workflows/build-ubuntu_pyqt5.yml
.github/workflows/build-windows_pyqt5.yml
.github/workflows/build-windows_pyqt6.yml
.github/workflows/inactive-issues.yml
envs/conda_env_headless.yml
envs/requirements_headless.txt
examples/__init__.py
examples/images/mitochondria/ASY15-1_0nM-10_s10_mNeon.tif
examples/images/mitochondria/ASY15-1_0nM-10_s10_segm.npz
examples/ini_config_files_templates/example_config_params_mitochondria.ini
examples/ini_config_files_templates/example_config_params_smFISH.ini
examples/ini_config_files_templates/mtDNA_yeast_tutorial_parameters.ini
examples/ini_config_files_templates/smFISH_yeast_tutorial_parameters.ini
examples/notebooks/spots_synthetic_simple.ipynb
examples/scripts/spots_synthetic_simple.py
examples/test_data_gui/mito_mtDNA_yeast/SpotMAX_test_gui_example_parameters.ini
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_acdc_output.csv
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_mKate.tif
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_mNeon.tif
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_metadata.csv
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_phase_contr.tif
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_segm.npz
examples/test_data_gui/mito_mtDNA_yeast/Position_16/Images/ASY15-1_15nM-16_s16_segmInfo.csv
spotmax/__init__.py
spotmax/__main__.py
spotmax/_debug.py
spotmax/_process.py
spotmax/_run.py
spotmax/_version.py
spotmax/_warnings.py
spotmax/colors.py
spotmax/config.py
spotmax/core.py
spotmax/data.py
spotmax/dialogs.py
spotmax/features.py
spotmax/filters.py
spotmax/gui.py
spotmax/html_func.py
spotmax/io.py
spotmax/palettes.py
spotmax/pipe.py
spotmax/prompts.py
spotmax/qtworkers.py
spotmax/resources.qrc
spotmax/scores.py
spotmax/transformations.py
spotmax/tune.py
spotmax/utils.py
spotmax/widgets.py
spotmax.egg-info/PKG-INFO
spotmax.egg-info/SOURCES.txt
spotmax.egg-info/dependency_links.txt
spotmax.egg-info/entry_points.txt
spotmax.egg-info/requires.txt
spotmax.egg-info/top_level.txt
spotmax/BioImageIO/__init__.py
spotmax/BioImageIO/create_model_resource.ipynb
spotmax/BioImageIO/model.py
spotmax/BioImageIO/test_any_model_gui.py
spotmax/BioImageIO/test_any_model_script.py
spotmax/BioImageIO/SpotMAX_UNet_3D/README.md
spotmax/BioImageIO/SpotMAX_UNet_3D/_sphere_3d.svg
spotmax/BioImageIO/SpotMAX_UNet_3D/config.yaml
spotmax/BioImageIO/SpotMAX_UNet_3D/cover.png
spotmax/BioImageIO/SpotMAX_UNet_3D/cover.svg
spotmax/BioImageIO/SpotMAX_UNet_3D/create_3d_sphere_surface.py
spotmax/BioImageIO/SpotMAX_UNet_3D/create_cover_image.py
spotmax/BioImageIO/SpotMAX_UNet_3D/create_io_samples.py
spotmax/BioImageIO/SpotMAX_UNet_3D/environment.yml
spotmax/BioImageIO/SpotMAX_UNet_3D/input_sample.npy
spotmax/BioImageIO/SpotMAX_UNet_3D/model_usage.py
spotmax/BioImageIO/SpotMAX_UNet_3D/output_sample_mask.npy
spotmax/Spotiflow/__init__.py
spotmax/Spotiflow/spotiflow_smax_model.py
spotmax/docs/Makefile
spotmax/docs/__init__.py
spotmax/docs/make.bat
spotmax/docs/requirements.txt
spotmax/docs/source/__init__.py
spotmax/docs/source/conf.py
spotmax/docs/source/index.rst
spotmax/docs/source/api/api.rst
spotmax/docs/source/features/_background_description.rst
spotmax/docs/source/features/_effect_size_Cohen_formula.rst
spotmax/docs/source/features/_effect_size_Glass_formula.rst
spotmax/docs/source/features/_effect_size_Hedge_formula.rst
spotmax/docs/source/features/_effect_size_description.rst
spotmax/docs/source/features/aggr_features_description.rst
spotmax/docs/source/features/index.rst
spotmax/docs/source/features/ref_ch_features_description.rst
spotmax/docs/source/features/single_spot_features_description.rst
spotmax/docs/source/how_it_works/index.rst
spotmax/docs/source/how_it_works/ref_ch_segm.rst
spotmax/docs/source/how_it_works/spot_detect.rst
spotmax/docs/source/how_it_works/spot_pred.rst
spotmax/docs/source/how_it_works/spot_quant.rst
spotmax/docs/source/install/_conda_create_activate_acdc.rst
spotmax/docs/source/install/_gui_packages.rst
spotmax/docs/source/install/_install_conda_open_terminal.rst
spotmax/docs/source/install/_install_numba.rst
spotmax/docs/source/install/cuda.rst
spotmax/docs/source/install/hpc.rst
spotmax/docs/source/install/index.rst
spotmax/docs/source/install/latest.rst
spotmax/docs/source/install/source.rst
spotmax/docs/source/install/stable.rst
spotmax/docs/source/misc/cite.rst
spotmax/docs/source/misc/contributing.rst
spotmax/docs/source/misc/get_started.rst
spotmax/docs/source/misc/logos.rst
spotmax/docs/source/misc/output_files.rst
spotmax/docs/source/misc/publications.rst
spotmax/docs/source/misc/training_ai.rst
spotmax/docs/source/parameters/ai_params.rst
spotmax/docs/source/parameters/index.rst
spotmax/docs/source/parameters/parameters_description.rst
spotmax/docs/source/parameters/parameters_tuning.rst
spotmax/docs/source/run/index.rst
spotmax/docs/source/run/run_cli.rst
spotmax/docs/source/run/run_py_pkg.rst
spotmax/docs/source/run/gui/analysis_parameters_tab.rst
spotmax/docs/source/run/gui/index.rst
spotmax/docs/source/run/gui/inspect_results_tab.rst
spotmax/docs/source/run/gui/tune_parameters_tab.rst
spotmax/docs/source/tutorials/_preliminary_segment_cells.rst
spotmax/docs/source/tutorials/index.rst
spotmax/docs/source/tutorials/mtDNA_yeast.rst
spotmax/docs/source/tutorials/smFISH_yeast.rst
spotmax/html_files/gui_welcome.html
spotmax/nnet/__init__.py
spotmax/nnet/_predict_single_image.py
spotmax/nnet/config.yaml
spotmax/nnet/model.py
spotmax/nnet/preprocess.py
spotmax/nnet/transform.py
spotmax/nnet/data/single_image.tiff
spotmax/nnet/data/single_label.tiff
spotmax/nnet/data/single_volume.tiff
spotmax/nnet/data/single_volume_label.tiff
spotmax/nnet/models/__init__.py
spotmax/nnet/models/base_model.py
spotmax/nnet/models/nd_model.py
spotmax/nnet/models/unet2d_model.py
spotmax/nnet/models/unet3D_model.py
spotmax/nnet/models/unet2D/__init__.py
spotmax/nnet/models/unet2D/dice_score.py
spotmax/nnet/models/unet2D/unet_2D_model.py
spotmax/nnet/models/unet2D/unet_parts.py
spotmax/nnet/models/unet3D/__init__.py
spotmax/nnet/models/unet3D/__version__.py
spotmax/nnet/models/unet3D/augment/__init__.py
spotmax/nnet/models/unet3D/augment/transformer-test.ipynb
spotmax/nnet/models/unet3D/augment/transforms.py
spotmax/nnet/models/unet3D/datasets/__init__.py
spotmax/nnet/models/unet3D/datasets/hdf5.py
spotmax/nnet/models/unet3D/datasets/utils.py
spotmax/nnet/models/unet3D/unet3d/__init__.py
spotmax/nnet/models/unet3D/unet3d/buildingblocks.py
spotmax/nnet/models/unet3D/unet3d/losses.py
spotmax/nnet/models/unet3D/unet3d/metrics.py
spotmax/nnet/models/unet3D/unet3d/model.py
spotmax/nnet/models/unet3D/unet3d/predictor.py
spotmax/nnet/models/unet3D/unet3d/trainer.py
spotmax/nnet/models/unet3D/unet3d/utils.py
spotmax/resources/spotMAX_icon.ico
spotmax/resources/spotMAX_logo.png
spotmax/resources/spotMAX_logo.svg
spotmax/resources/spotmax_v1_paramWin.png
spotmax/resources/spotmax_v2_parameters.png
spotmax/resources/icons/cog.svg
spotmax/resources/icons/cog_play.svg
spotmax/resources/icons/math/add.svg
tests/test_import_spotmax.py