Index

_

__call__() (HuggingMouse.pipelines.base.Pipeline method) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method) (HuggingMouse.pipelines.single_trial_fs.MovieSingleTrialRegressionAnalysis method)

__version__ (in module HuggingMouse)

A

agent module agent (in module agent)

allen_cache_path (HuggingMouse.make_embeddings.MakeEmbeddings attribute) allen_engine() (in module mousetool) AllenCachePathNotSpecifiedError AllenExperimentUtility (class in HuggingMouse.allen_api_utilities)

B

boc (HuggingMouse.allen_api_utilities.AllenExperimentUtility attribute) (HuggingMouse.make_embeddings.MakeEmbeddings attribute) (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) (HuggingMouse.trial_averaged_data.MakeTrialAveragedData attribute)

C

cache (in module templ)

cre_line_info() (HuggingMouse.allen_api_utilities.AllenExperimentUtility method)

D

df_one_more_repeats (in module templ)

dim_reduction_model (HuggingMouse.visualizers.VisualizerDimReduction attribute) dropna() (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method)

E

eid_dict (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) (HuggingMouse.trial_averaged_data.MakeTrialAveragedData attribute)

execute() (HuggingMouse.make_embeddings.MakeEmbeddings method) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor method) experiment_container_ids_imaged_areas() (HuggingMouse.allen_api_utilities.AllenExperimentUtility method)

F

fc1 (HuggingMouse.pipelines.multitrial_regression.ZIGRegression attribute) fc2 (HuggingMouse.pipelines.multitrial_regression.ZIGRegression attribute) fc_p (HuggingMouse.pipelines.multitrial_regression.ZIGRegression attribute) fc_theta (HuggingMouse.pipelines.multitrial_regression.ZIGRegression attribute)

filter_data() (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method) forward() (HuggingMouse.pipelines.multitrial_regression.ZIGRegression method) func_session (in module templ) functional_conn_session (in module templ)

G

generate_random_state() (in module HuggingMouse.utils)

get_data() (HuggingMouse.trial_averaged_data.MakeTrialAveragedData method) get_spikes_in_intervals_optimized() (in module templ)

H

handle_single_session() (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method) hash_df() (in module HuggingMouse.utils) heatmap() (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method) HuggingMouse module HuggingMouse.allen_api_utilities module HuggingMouse.custom_exceptions module HuggingMouse.make_embeddings module HuggingMouse.pipelines module HuggingMouse.pipelines.base module

HuggingMouse.pipelines.multitrial_regression module HuggingMouse.pipelines.neuron_prediction module HuggingMouse.pipelines.pipeline_tasks module HuggingMouse.pipelines.single_trial_fs module HuggingMouse.regressors module HuggingMouse.trial_averaged_data module HuggingMouse.utils module HuggingMouse.visualizers module

I

info() (HuggingMouse.visualizers.VisualizerDimReduction method)

L

logk (HuggingMouse.pipelines.multitrial_regression.ZIGRegression attribute)

M

make_container_dict() (in module HuggingMouse.utils) make_regression_data() (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor method) make_single_session_data() (HuggingMouse.trial_averaged_data.MakeTrialAveragedData method) MakeEmbeddings (class in HuggingMouse.make_embeddings) MakeTrialAveragedData (class in HuggingMouse.trial_averaged_data) manifest_path (in module templ) message (HuggingMouse.custom_exceptions.AllenCachePathNotSpecifiedError attribute) (HuggingMouse.custom_exceptions.RegressionOutputCachePathNotSpecifiedError attribute) (HuggingMouse.custom_exceptions.TransformerEmbeddingCachePathNotSpecifiedError attribute) metrics (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) model (HuggingMouse.make_embeddings.MakeEmbeddings attribute) (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) model_name_str (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) model_prefix (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) module agent HuggingMouse HuggingMouse.allen_api_utilities HuggingMouse.custom_exceptions HuggingMouse.make_embeddings HuggingMouse.pipelines HuggingMouse.pipelines.base HuggingMouse.pipelines.multitrial_regression HuggingMouse.pipelines.neuron_prediction HuggingMouse.pipelines.pipeline_tasks HuggingMouse.pipelines.single_trial_fs HuggingMouse.regressors HuggingMouse.trial_averaged_data HuggingMouse.utils HuggingMouse.visualizers mousetool templ

mousetool module movie_one_dataset (HuggingMouse.make_embeddings.MakeEmbeddings attribute) movie_three_dataset (HuggingMouse.make_embeddings.MakeEmbeddings attribute) movie_two_dataset (HuggingMouse.make_embeddings.MakeEmbeddings attribute) MovieSingleTrialRegressionAnalysis (class in HuggingMouse.pipelines.single_trial_fs) MultiTrialRegressionPipeline (class in HuggingMouse.pipelines.multitrial_regression)

N

NeuronPredictionPipeline (class in HuggingMouse.pipelines.neuron_prediction)

O

output_dir (in module templ)

P

Pipeline (class in HuggingMouse.pipelines.base) pipeline() (in module HuggingMouse.pipelines.pipeline_tasks) process_single_trial() (in module HuggingMouse.utils) process_stims() (HuggingMouse.make_embeddings.MakeEmbeddings method)

processor (HuggingMouse.make_embeddings.MakeEmbeddings attribute) (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute)

R

random_state_dct (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) raw_data_dct (HuggingMouse.make_embeddings.MakeEmbeddings attribute) regr_analysis_results_cache (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) regression() (HuggingMouse.pipelines.single_trial_fs.MovieSingleTrialRegressionAnalysis method) (in module HuggingMouse.utils)

regression_model (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) regression_model_class (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) RegressionOutputCachePathNotSpecifiedError

S

save_to_cache() (HuggingMouse.make_embeddings.MakeEmbeddings method) scatter_movies() (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline method) session_A (HuggingMouse.make_embeddings.MakeEmbeddings attribute) session_B (HuggingMouse.make_embeddings.MakeEmbeddings attribute) session_C (HuggingMouse.make_embeddings.MakeEmbeddings attribute) single_trial_f (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute)

stimuli_df (in module templ) stimuli_of_interest (in module templ) stimulus_session_dict (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute) (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor attribute) (HuggingMouse.trial_averaged_data.MakeTrialAveragedData attribute) (HuggingMouse.visualizers.VisualizerDimReduction attribute)

T

templ module test_set_size (HuggingMouse.pipelines.multitrial_regression.MultiTrialRegressionPipeline attribute) (HuggingMouse.pipelines.neuron_prediction.NeuronPredictionPipeline attribute)

train_test_split() (HuggingMouse.pipelines.single_trial_fs.MovieSingleTrialRegressionAnalysis method) train_test_split_interleaved() (HuggingMouse.pipelines.single_trial_fs.MovieSingleTrialRegressionAnalysis method) transformer_embedding_cache_path (HuggingMouse.make_embeddings.MakeEmbeddings attribute) TransformerEmbeddingCachePathNotSpecifiedError

U

update_data_index_df() (HuggingMouse.regressors.VisionEmbeddingToNeuronsRegressor method)

V

view_all_cre_lines() (HuggingMouse.allen_api_utilities.AllenExperimentUtility method) view_all_imaged_areas() (HuggingMouse.allen_api_utilities.AllenExperimentUtility method) VisionEmbeddingToNeuronsRegressor (class in HuggingMouse.regressors)

visual_areas_info() (HuggingMouse.allen_api_utilities.AllenExperimentUtility method) visualize() (HuggingMouse.visualizers.VisualizerDimReduction method) VisualizerDimReduction (class in HuggingMouse.visualizers)

Z

ZIGRegression (class in HuggingMouse.pipelines.multitrial_regression)