Setup Part 1: Clone the Repository

Execute git clone https://github.com/AllenInstitute/HebbsVision, or otherwise clone https://github.com/AllenInstitute/HebbsVision into a directory of your choice. If your cloning method supports git large files, this should take a while and download gigs of files.

Setup Part 2: Environment Setup

First, ensure that anaconda (conda) is installed on your system. Then, to create the environment and install the conda and pip packages, at a command prompt execute conda env create -n HebbsVision -f conda_files.yaml In the case of failure installing NeuroAnalysisTools, due to the lack of requirements.txt, you must create the environment first then download NeuroAnalysisTools from https://github.com/zhuangjun1981/NeuroAnalysisTools. Once it exists in a local directory, you can install it locally from pip with pip install -e ./<path_to_NeuroAnalysisTools>. The same workaround can be employed with V1DD-Physiology (https://github.com/AllenInstitute/v1dd_physiology) if a similar error occurs.

The LSMM library must be installed via a local wheel file at the moment, and the .whl is included in the root of the repository. Install it with pip install lsmm_data-0.1.2-py2.py3-none-any.whl

Assembly Extraction and Hyperparameter Tuning (Optional):

Note that this step can take some time, so for those simply interested in reproducing our analysis of the extracted assemblies, the HebbsVision repository includes all the hyperparameter files that were generated using Scan 1-4 data following the instructions in Molter et al. 2024: "Similarity Graph Clustering for Neural Assembly Detection" p. 175, and we also include the file generated from Scan 1-3 (the scan on which the remaining analysis is focused) using the selected best hyperparameters.

Figure 1

To recreate panel B of figure 1 (the only one displaying data from our analysis), open FigureCode/Figure1/Figure1.ipynb and execute all the cells in order. It will create files in the FigureCode/Figure1/ directory.

• Figure 1B uses FigureCode/Figure1/3D_Scan_Images.png, FigureCode/Figure1/Example_Activity_Traces.png, and FigureCode/Figure1/raster_plot_red.png.

Figure 2

To recreate panels B, C, D, and the data for panel E of figure 2, open FigureCode/Figure2/Figure2.ipynb and execute all the cells in order.
It will create files in the FigureCode/Figure2/ directory.

• Figure 2B uses FigureCode/Figure2/Assemblies_Intersection_Upset_Plot.png.
• Figure 2C uses FigureCode/Figure2/Assemblies_Plotted_In_Recording_Space_Same_Plot.png.
• Figure 2D uses FigureCode/Figure2/Spatial_Distribution_of_Cells_by_Assembly.png.
• The data for Figure 2E are printed in the .ipynb notebook, following the cell where compare_assemblies_spatial_distribution is called.

Figure 3

To recreate all panels in Figure 3, open FigureCode/Figure3/Figure3.ipynb and execute all the cells in order. It will create files in the FigureCode/Figure3/ directory.

• Figure 3A uses FigureCode/Figure3/correlations_assemblies_vs_random_ensembles_raincould_plot.png
• Figure 3B uses FigureCode/Figure3/sparsity_with_Gini_coefficient_by_assembly_and_random_ensembles.png
• Figure 3C uses FigureCode/Figure3/oracle_scores_dff_all_sets_raincloud.png
• Figure 3D uses FigureCode/Figure3/assembly_balanced_clip_id_percentage_decoder_MLPClassifier.png
• Figure 3E uses FigureCode/Figure3/random_ensemble_balanced_clip_id_percentage_decoder_MLPClassifier.png
• Figure 3F uses FigureCode/Figure3/Trigger_Frame_Assembly_4_real_assemblies_mean_trigger_frame.png, FigureCode/Figure3/Trigger_Frame_Assembly_4_random_ensembles_mean_trigger_frame.png, and FigureCode/Figure3/Trigger_Frame_Assembly_4_difference_squared_in_mean_trigger_frame_assembly_minus_random.png

Figure 4

To recreate all panels in Figure 4, open FigureCode/Figure4/Figure4_Master.ipynb and execute all the cells in order. It will create files in the FigureCode/Figure4/ directory.

• Figure 4A uses FigureCode/Figure4/connectivity_plot_final.png
• Figure 4B uses FigureCode/Figure4/draft_figures/Betweenness_Centrality_All.png
• Figure 4C uses FigureCode/Figure4/draft_figures/Outdegree_Centrality_All.png
• Figure 4D uses FigureCode/Figure4/draft_figures/A_No_A_Prob_Conn_by_Conn_Type_v2.png and FigureCode/Figure4/draft_figures/Prob_Conn_by_Conn_Type_v2.png
• Figure 4E uses FigureCode/Figure4/draft_figures/Nonzero_PSD_by_Conn_with_side_plot.png
• Figure 4F uses FigureCode/Figure4/draft_figures/A_No_A_Prob_Conn_by_Conn_Type_E_Chains_v2.png and FigureCode/Figure4/draft_figures/Prob_Conn_by_Conn_Type_E_Chains_v2.png
• Figure 4G uses FigureCode/Figure4/draft_figures/Nonzero_PSD_by_Conn_E_Chain_with_side_plot.png
• Figure 4H uses FigureCode/Figure4/draft_figures/A_No_A_Prob_Conn_by_Conn_Type_I_Chains_v2.png and FigureCode/Figure4/draft_figures/Prob_Conn_by_Conn_Type_I_Chains_v2.png
• Figure 4I uses FigureCode/Figure4/draft_figures/Nonzero_PSD_by_Conn_I_Chain_with_side_plot.png

Additional tests referenced in the statistical table are printed out throughout the .ipynb files above as they are run.