LICENSE.txt
MANIFEST.in
Makefile
README.md
doc_requirements.txt
requirements.txt
setup.cfg
setup.py
test_requirements.txt
allensdk/__init__.py
allensdk/deprecated.py
allensdk.egg-info/PKG-INFO
allensdk.egg-info/SOURCES.txt
allensdk.egg-info/dependency_links.txt
allensdk.egg-info/requires.txt
allensdk.egg-info/top_level.txt
allensdk/api/__init__.py
allensdk/api/api.py
allensdk/api/cache.py
allensdk/api/queries/__init__.py
allensdk/api/queries/annotated_section_data_sets_api.py
allensdk/api/queries/biophysical_api.py
allensdk/api/queries/brain_observatory_api.py
allensdk/api/queries/cell_types_api.py
allensdk/api/queries/connected_services.py
allensdk/api/queries/glif_api.py
allensdk/api/queries/grid_data_api.py
allensdk/api/queries/image_download_api.py
allensdk/api/queries/mouse_atlas_api.py
allensdk/api/queries/mouse_connectivity_api.py
allensdk/api/queries/ontologies_api.py
allensdk/api/queries/reference_space_api.py
allensdk/api/queries/rma_api.py
allensdk/api/queries/rma_pager.py
allensdk/api/queries/rma_template.py
allensdk/api/queries/svg_api.py
allensdk/api/queries/synchronization_api.py
allensdk/api/queries/tree_search_api.py
allensdk/brain_observatory/__init__.py
allensdk/brain_observatory/brain_observatory_exceptions.py
allensdk/brain_observatory/brain_observatory_plotting.py
allensdk/brain_observatory/circle_plots.py
allensdk/brain_observatory/demixer.py
allensdk/brain_observatory/dff.py
allensdk/brain_observatory/drifting_gratings.py
allensdk/brain_observatory/findlevel.py
allensdk/brain_observatory/locally_sparse_noise.py
allensdk/brain_observatory/natural_movie.py
allensdk/brain_observatory/natural_scenes.py
allensdk/brain_observatory/observatory_plots.py
allensdk/brain_observatory/r_neuropil.py
allensdk/brain_observatory/roi_masks.py
allensdk/brain_observatory/session_analysis.py
allensdk/brain_observatory/static_gratings.py
allensdk/brain_observatory/stimulus_analysis.py
allensdk/brain_observatory/stimulus_info.py
allensdk/brain_observatory/receptive_field_analysis/__init__.py
allensdk/brain_observatory/receptive_field_analysis/chisquarerf.py
allensdk/brain_observatory/receptive_field_analysis/eventdetection.py
allensdk/brain_observatory/receptive_field_analysis/fit_parameters.py
allensdk/brain_observatory/receptive_field_analysis/fitgaussian2D.py
allensdk/brain_observatory/receptive_field_analysis/postprocessing.py
allensdk/brain_observatory/receptive_field_analysis/receptive_field.py
allensdk/brain_observatory/receptive_field_analysis/tools.py
allensdk/brain_observatory/receptive_field_analysis/utilities.py
allensdk/brain_observatory/receptive_field_analysis/visualization.py
allensdk/config/__init__.py
allensdk/config/manifest.py
allensdk/config/manifest_builder.py
allensdk/config/app/__init__.py
allensdk/config/app/application_config.py
allensdk/config/app/logging.conf
allensdk/config/model/__init__.py
allensdk/config/model/description.py
allensdk/config/model/description_parser.py
allensdk/config/model/formats/__init__.py
allensdk/config/model/formats/hdf5_util.py
allensdk/config/model/formats/json_description_parser.py
allensdk/config/model/formats/pycfg_description_parser.py
allensdk/core/__init__.py
allensdk/core/brain_observatory_cache.py
allensdk/core/brain_observatory_nwb_data_set.py
allensdk/core/cell_types_cache.py
allensdk/core/dat_utilities.py
allensdk/core/h5_utilities.py
allensdk/core/json_utilities.py
allensdk/core/mouse_connectivity_cache.py
allensdk/core/nwb_data_set.py
allensdk/core/obj_utilities.py
allensdk/core/ontology.py
allensdk/core/reference_space.py
allensdk/core/reference_space_cache.py
allensdk/core/simple_tree.py
allensdk/core/sitk_utilities.py
allensdk/core/structure_tree.py
allensdk/core/swc.py
allensdk/ephys/__init__.py
allensdk/ephys/ephys_extractor.py
allensdk/ephys/ephys_features.py
allensdk/ephys/extract_cell_features.py
allensdk/ephys/feature_extractor.py
allensdk/internal/__init__.py
allensdk/internal/api/__init__.py
allensdk/internal/api/queries/__init__.py
allensdk/internal/api/queries/biophysical_module_api.py
allensdk/internal/api/queries/biophysical_module_reader.py
allensdk/internal/api/queries/optimize_config_reader.py
allensdk/internal/api/queries/pre_release.py
allensdk/internal/brain_observatory/__init__.py
allensdk/internal/brain_observatory/annotated_region_metrics.py
allensdk/internal/brain_observatory/demix_report.py
allensdk/internal/brain_observatory/demixer.py
allensdk/internal/brain_observatory/eye_calibration.py
allensdk/internal/brain_observatory/fit_ellipse.py
allensdk/internal/brain_observatory/frame_stream.py
allensdk/internal/brain_observatory/itracker.py
allensdk/internal/brain_observatory/itracker_utils.py
allensdk/internal/brain_observatory/mask_set.py
allensdk/internal/brain_observatory/ophys_session_decomposition.py
allensdk/internal/brain_observatory/roi_filter.py
allensdk/internal/brain_observatory/roi_filter_utils.py
allensdk/internal/brain_observatory/run_itracker.py
allensdk/internal/brain_observatory/resources/__init__.py
allensdk/internal/brain_observatory/resources/roi_filter_training_criteria.json
allensdk/internal/core/__init__.py
allensdk/internal/core/lims_pipeline_module.py
allensdk/internal/core/lims_utilities.py
allensdk/internal/core/simpletree.py
allensdk/internal/core/swc.py
allensdk/internal/docker/lims/neuronal_model_run_files.py
allensdk/internal/docker/neuron_base/requirements.txt
allensdk/internal/docker/neuron_base/test_requirements.txt
allensdk/internal/ephys/__init__.py
allensdk/internal/ephys/core_feature_extract.py
allensdk/internal/ephys/plot_qc_figures.py
allensdk/internal/ephys/plot_qc_figures3.py
allensdk/internal/model/AIC.py
allensdk/internal/model/GLM.py
allensdk/internal/model/__init__.py
allensdk/internal/model/data_access.py
allensdk/internal/model/biophysical/__init__.py
allensdk/internal/model/biophysical/biophysical_archiver.py
allensdk/internal/model/biophysical/check_fi_shift.py
allensdk/internal/model/biophysical/deap_utils.py
allensdk/internal/model/biophysical/ephys_utils.py
allensdk/internal/model/biophysical/fit_stage_1.py
allensdk/internal/model/biophysical/fit_stage_2.py
allensdk/internal/model/biophysical/make_deap_fit_json.py
allensdk/internal/model/biophysical/neuron_parallel.py
allensdk/internal/model/biophysical/optimize.py
allensdk/internal/model/biophysical/run_optimize.py
allensdk/internal/model/biophysical/run_optimize.sh
allensdk/internal/model/biophysical/run_optimize_workflow.py
allensdk/internal/model/biophysical/run_passive_fit.py
allensdk/internal/model/biophysical/run_simulate.sh
allensdk/internal/model/biophysical/run_simulate_lims.py
allensdk/internal/model/biophysical/run_simulate_workflow.py
allensdk/internal/model/biophysical/fits/__init__.py
allensdk/internal/model/biophysical/fits/config_base.json
allensdk/internal/model/biophysical/fits/fit_styles/__init__.py
allensdk/internal/model/biophysical/fits/fit_styles/f12_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f12_noapic_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f13_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f13_noapic_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f6_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f6_noapic_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f9_fit_style.json
allensdk/internal/model/biophysical/fits/fit_styles/f9_noapic_fit_style.json
allensdk/internal/model/biophysical/passive_fitting/__init__.py
allensdk/internal/model/biophysical/passive_fitting/neuron_passive_fit.py
allensdk/internal/model/biophysical/passive_fitting/neuron_passive_fit2.py
allensdk/internal/model/biophysical/passive_fitting/neuron_passive_fit_elec.py
allensdk/internal/model/biophysical/passive_fitting/neuron_utils.py
allensdk/internal/model/biophysical/passive_fitting/output_grabber.py
allensdk/internal/model/biophysical/passive_fitting/preprocess.py
allensdk/internal/model/biophysical/passive_fitting/passive/__init__.py
allensdk/internal/model/glif/ASGLM.py
allensdk/internal/model/glif/MLIN.py
allensdk/internal/model/glif/__init__.py
allensdk/internal/model/glif/are_two_lists_of_arrays_the_same.py
allensdk/internal/model/glif/configure_model.py
allensdk/internal/model/glif/error_functions.py
allensdk/internal/model/glif/find_spikes.py
allensdk/internal/model/glif/find_sweeps.py
allensdk/internal/model/glif/glif_experiment.py
allensdk/internal/model/glif/glif_optimizer.py
allensdk/internal/model/glif/glif_optimizer_neuron.py
allensdk/internal/model/glif/optimize_neuron.py
allensdk/internal/model/glif/plotting.py
allensdk/internal/model/glif/preprocess_neuron.py
allensdk/internal/model/glif/rc.py
allensdk/internal/model/glif/spike_cutting.py
allensdk/internal/model/glif/threshold_adaptation.py
allensdk/internal/morphology/__init__.py
allensdk/internal/morphology/compartment.py
allensdk/internal/morphology/morphology.py
allensdk/internal/morphology/morphvis.py
allensdk/internal/morphology/node.py
allensdk/internal/morphology/validate_swc.py
allensdk/internal/mouse_connectivity/__init__.py
allensdk/internal/mouse_connectivity/interval_unionize/__init__.py
allensdk/internal/mouse_connectivity/interval_unionize/cav_unionize.py
allensdk/internal/mouse_connectivity/interval_unionize/cav_unionizer.py
allensdk/internal/mouse_connectivity/interval_unionize/data_utilities.py
allensdk/internal/mouse_connectivity/interval_unionize/interval_unionizer.py
allensdk/internal/mouse_connectivity/interval_unionize/run_tissuecyte_unionize_cav.py
allensdk/internal/mouse_connectivity/interval_unionize/run_tissuecyte_unionize_classic.py
allensdk/internal/mouse_connectivity/interval_unionize/tissuecyte_unionize_record.py
allensdk/internal/mouse_connectivity/interval_unionize/tissuecyte_unionizer.py
allensdk/internal/mouse_connectivity/interval_unionize/unionize_record.py
allensdk/internal/mouse_connectivity/projection_thumbnail/__init__.py
allensdk/internal/mouse_connectivity/projection_thumbnail/generate_projection_strip.py
allensdk/internal/mouse_connectivity/projection_thumbnail/image_sheet.py
allensdk/internal/mouse_connectivity/projection_thumbnail/projection_functions.py
allensdk/internal/mouse_connectivity/projection_thumbnail/visualization_utilities.py
allensdk/internal/mouse_connectivity/projection_thumbnail/volume_projector.py
allensdk/internal/mouse_connectivity/projection_thumbnail/volume_utilities.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/__init__.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/base_subimage.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/cav_subimage.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/classic_subimage.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/downsampling_utilities.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/image_series_gridder.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/image_utilities.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/run_cav.py
allensdk/internal/mouse_connectivity/tissuecyte_gridding/run_classic.py
allensdk/internal/mouse_connectivity/tissuecyte_stitching/__init__.py
allensdk/internal/mouse_connectivity/tissuecyte_stitching/stitcher.py
allensdk/internal/mouse_connectivity/tissuecyte_stitching/tile.py
allensdk/internal/pipeline_modules/__init__.py
allensdk/internal/pipeline_modules/run_annotated_region_metrics.py
allensdk/internal/pipeline_modules/run_demixing.py
allensdk/internal/pipeline_modules/run_eye_tracking.py
allensdk/internal/pipeline_modules/run_neuropil_correction.py
allensdk/internal/pipeline_modules/run_observatory_analysis.py
allensdk/internal/pipeline_modules/run_observatory_container_thumbnails.py
allensdk/internal/pipeline_modules/run_observatory_thumbnails.py
allensdk/internal/pipeline_modules/run_ophys_eye_calibration.py
allensdk/internal/pipeline_modules/run_ophys_session_decomposition.py
allensdk/internal/pipeline_modules/run_ophys_trace_extraction.py
allensdk/internal/pipeline_modules/run_roi_filter.py
allensdk/internal/pipeline_modules/run_tissuecyte_grid_cav_from_json.py
allensdk/internal/pipeline_modules/run_tissuecyte_grid_classic_from_json.py
allensdk/internal/pipeline_modules/run_tissuecyte_projection_thumbnail_from_json.py
allensdk/internal/pipeline_modules/run_tissuecyte_stitching_classic.py
allensdk/internal/pipeline_modules/run_tissuecyte_unionize_cav_from_json.py
allensdk/internal/pipeline_modules/run_tissuecyte_unionize_classic_from_json.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/convert_igor_nwb.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/extract_nwb_data.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/feature_extraction_module.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/lab_notebook_reader.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/nwb_publish.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/qc.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/qc_support.py
allensdk/internal/pipeline_modules/IVSCC/ephys_nwb/resource_file.py
allensdk/internal/pipeline_modules/cell_types/morphology/calculate_features.py
allensdk/internal/pipeline_modules/cell_types/morphology/cortical_layers.py
allensdk/internal/pipeline_modules/cell_types/morphology/surrogate_strategy.py
allensdk/internal/pipeline_modules/cell_types/morphology/upright_transform.py
allensdk/internal/pipeline_modules/gbm/__init__.py
allensdk/internal/pipeline_modules/gbm/generate_gbm_analysis_run_records.py
allensdk/internal/pipeline_modules/gbm/generate_gbm_heatmap.py
allensdk/internal/pipeline_modules/gbm/generate_gbm_sample_metadata.py
allensdk/model/__init__.py
allensdk/model/biophys_sim/__init__.py
allensdk/model/biophys_sim/bps_command.py
allensdk/model/biophys_sim/config.py
allensdk/model/biophys_sim/logging.conf
allensdk/model/biophys_sim/manifest_default.json
allensdk/model/biophys_sim/neuron/__init__.py
allensdk/model/biophys_sim/neuron/hoc_utils.py
allensdk/model/biophys_sim/scripts/__init__.py
allensdk/model/biophys_sim/scripts/bps
allensdk/model/biophysical/__init__.py
allensdk/model/biophysical/logging.conf
allensdk/model/biophysical/run_simulate.py
allensdk/model/biophysical/runner.py
allensdk/model/biophysical/utils.py
allensdk/model/glif/__init__.py
allensdk/model/glif/glif_neuron.py
allensdk/model/glif/glif_neuron_methods.py
allensdk/model/glif/simulate_neuron.py
allensdk/morphology/__init__.py
allensdk/morphology/validate_swc.py
allensdk/test/glif_tests.py
allensdk/test/test_deprecated.py
allensdk/test/test_inline_examples.py
allensdk/test/test_temp_dir.py
allensdk/test/api/test_annotated_section_data_set_api.py
allensdk/test/api/test_api.py
allensdk/test/api/test_biophysical_api.py
allensdk/test/api/test_brain_observatory_api.py
allensdk/test/api/test_cache.py
allensdk/test/api/test_cacheable.py
allensdk/test/api/test_cell_types_api.py
allensdk/test/api/test_file_download.py
allensdk/test/api/test_glif_api.py
allensdk/test/api/test_grid_data_api.py
allensdk/test/api/test_image_download_api.py
allensdk/test/api/test_mouse_atlas_api.py
allensdk/test/api/test_mouse_connectivity_api.py
allensdk/test/api/test_ontologies_api.py
allensdk/test/api/test_pager.py
allensdk/test/api/test_reference_space_api.py
allensdk/test/api/test_rma_template.py
allensdk/test/api/test_svg_api.py
allensdk/test/api/test_synchronization_api.py
allensdk/test/api/test_tree_search_api.py
allensdk/test/api/response_test_data/472451419_response.json
allensdk/test/brain_observatory/test_circle_plots.py
allensdk/test/brain_observatory/test_dff.py
allensdk/test/brain_observatory/test_drifting_gratings.py
allensdk/test/brain_observatory/test_locally_sparse_noise.py
allensdk/test/brain_observatory/test_natural_movie.py
allensdk/test/brain_observatory/test_natural_scenes.py
allensdk/test/brain_observatory/test_notebook.py
allensdk/test/brain_observatory/test_observatory_plots.py
allensdk/test/brain_observatory/test_observatory_plots_data.json
allensdk/test/brain_observatory/test_roi_masks.py
allensdk/test/brain_observatory/test_session_analysis.py
allensdk/test/brain_observatory/test_session_analysis_regression.py
allensdk/test/brain_observatory/test_session_analysis_regression_data.json
allensdk/test/brain_observatory/test_session_analysis_regression_data_list.json
allensdk/test/brain_observatory/test_static_gratings.py
allensdk/test/brain_observatory/test_stimulus_analysis.py
allensdk/test/brain_observatory/test_stimulus_info.py
allensdk/test/brain_observatory/receptive_field_analysis/test_chisquarerf.py
allensdk/test/brain_observatory/receptive_field_analysis/test_fitgaussian2D.py
allensdk/test/config/test_config_single_file_json.py
allensdk/test/config/test_json_comments.py
allensdk/test/config/test_manifest.py
allensdk/test/config/test_multi_file_config.py
allensdk/test/config/test_pyconfig_parser.py
allensdk/test/core/nwb_ephys_files.txt
allensdk/test/core/nwb_files.txt
allensdk/test/core/test_brain_observatory_cache.py
allensdk/test/core/test_brain_observatory_nwb_data_set.py
allensdk/test/core/test_cell_filters.py
allensdk/test/core/test_cell_types_cache_unit.py
allensdk/test/core/test_h5_utilities.py
allensdk/test/core/test_json_utilities.py
allensdk/test/core/test_mouse_connectivity_cache.py
allensdk/test/core/test_mouse_connectivity_notebook.py
allensdk/test/core/test_nwb_data_set.py
allensdk/test/core/test_obj_utilities.py
allensdk/test/core/test_reference_space.py
allensdk/test/core/test_reference_space_cache.py
allensdk/test/core/test_reference_space_notebook.py
allensdk/test/core/test_simple_tree.py
allensdk/test/core/test_sitk_utilities.py
allensdk/test/core/test_structure_tree.py
allensdk/test/ephys/test_extractor.py
allensdk/test/ephys/test_features.py
allensdk/test/ephys/data/spike_test_high_init_dvdt.txt
allensdk/test/ephys/data/spike_test_pair.txt
allensdk/test/ephys/data/spike_test_var_dt.txt
allensdk/test/model/test_biophysical_perisomatic.py
allensdk/test/model/test_glif.py
allensdk/test_utilities/__init__.py
allensdk/test_utilities/regression_fixture.py
allensdk/test_utilities/temp_dir.py