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:<br>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 stepsFile7 Data. TDE-RICA to the whole-brain activity dataset with different time-delay stepsFile8 Fig. Changes in neural activity induced by NaCl stimulationFile9 Fig. Cross-correlation functions of motif occurrences averaged across samples.File10 Fig. Determination of hyperparameters for gKDR-GMMFile11 Fig. Simulation results of gKDR-GMMFile12 Fig. Overview of simulation results of gKDR-GMMFile13 Fig. Lagged cross-correlation of all combinations of neurons for all samplesFile14 Fig. Activity profile of example neuron pairs with lagged correlationFile15 Fig. Simulation results by gKDR-GMM, evaluated by TDE-RICAFile16 Fig. Periodic mean of neuronal activities to visualize same periodicity as sensory inputFile17 Fig. Probabilistic and deterministic modelsFile18 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 representationFile21 Fig. Results of virtual optogenetics experimentsFile22 Fig. Number of “presynaptic neurons” used for the prediction modelsFile23 Fig. Outline of gKDR-GMMFile24 Fig. Simulation results by gKDR-GPThe 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)