Supplementary Materials for "Ensemble dynamics and information flow deduction from whole-brain imaging data"

This dataset is materials for a paper entitled "Ensemble dynamics and information flow deduction from whole-brain imaging data" (now in press at PLoS Comp Biol, https://doi.org/10.1371/journal.pcbi.1011848)

The preprint is on bioRxiv 2022.11.18.517011 (https://doi.org/10.1101/2022.11.18.517011)

This dataset includes following materials:

• File1 Fig. Result of 4D imaging in 24 samples.
• File2 Note. Demonstration of typical temporal dynamics extracted by TDE-RICA.
• File3 Fig. Results of TDE-RICA for 94 selected neurons of 10 selected samples.
• File4 Fig. Completing missing values by TDE-RICA by matrix factorization.
• File5 Fig. Results of TDE-RICA with matrix factorization for all 177 neurons of all 24 samples.
• File6 Note. TDE-RICA to simple time series data with different time-delay steps
• File7 Data. TDE-RICA to the whole-brain activity dataset with different time-delay steps
• File8 Fig. Changes in neural activity induced by NaCl stimulation
• File9 Fig. Cross-correlation functions of motif occurrences averaged across samples.
• File10 Fig. Determination of hyperparameters for gKDR-GMM
• File11 Fig. Simulation results of gKDR-GMM
• File12 Fig. Overview of simulation results of gKDR-GMM
• File13 Fig. Lagged cross-correlation of all combinations of neurons for all samples
• File14 Fig. Activity profile of example neuron pairs with lagged correlation
• File15 Fig. Simulation results by gKDR-GMM, evaluated by TDE-RICA
• File16 Fig. Periodic mean of neuronal activities to visualize same periodicity as sensory input
• File17 Fig. Probabilistic and deterministic models
• File18 Fig. Mean log likelihood values for each neuron in each sample.
• File19 Fig. Estimation of synaptic connection strength.
• File20 Fig. Mean synaptic weights from each sample are shown as graph representation
• File21 Fig. Results of virtual optogenetics experiments
• File22 Fig. Number of “presynaptic neurons” used for the prediction models
• File23 Fig. Outline of gKDR-GMM
• File24 Fig. Simulation results by gKDR-GP

The code for TDE-RICA will be found in the github repository (https://github.com/YuToyoshima/TDE-RICA)

The code for gKDR-GMM will be found in the github repository (https://github.com/yuichiiino1/gKDR-GMM).

The dataset used in these analysis will be found in the figshare repository (https://doi.org/10.6084/m9.figshare.21968078)