# Fast amortized inference of neural activity from calcium imaging data with variational autoencoders

@article{Speiser2017FastAI, title={Fast amortized inference of neural activity from calcium imaging data with variational autoencoders}, author={Artur Speiser and Jinyao Yan and Evan Archer and Lars Buesing and Srinivas C. Turaga and Jakob H. Macke}, journal={ArXiv}, year={2017}, volume={abs/1711.01846} }

Calcium imaging permits optical measurement of neural activity. [] Key Method The recognition network is trained to produce samples from the posterior distribution over spike trains. Once trained, performing inference amounts to a fast single forward pass through the network, without the need for iterative optimization or sampling.

## 44 Citations

### Community-based benchmarking improves spike rate inference from two-photon calcium imaging data

- Computer SciencePLoS Comput. Biol.
- 2018

The results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing, are reported, and the top-performing algorithms are based on a wide range of principles, yet provide highly correlated estimates of the neural activity.

### Community-based benchmarking improves spike inference from two-photon calcium imaging data

- Computer SciencebioRxiv
- 2017

The results of the spikefinder challenge, launched to catalyze the development of new spike inference algorithms through crowd-sourcing, are reported, and ten of the submitted algorithms are presented which show improved performance compared to previously evaluated methods.

### High frequency spike inference with particle Gibbs sampling

- Computer SciencebioRxiv
- 2022

This study introduces an auto-regressive generative model that accounts for bursting neuronal activity and baseline fluorescence modulation, and it also applies recent sequential Monte Carlo approaches to obtain joint posterior distributions of static and dynamic model parameters.

### Signal-to-signal neural networks for improved spike estimation from calcium imaging data

- Computer SciencebioRxiv
- 2020

A novel neural network-based data-driven algorithm that takes the fluorescence recording as the input and synthesizes the spike information signal, which is well-correlated with the actual spike positions, and outperforms state-of-the-art methods on standard evaluation framework.

### Scalable Spike Source Localization in Extracellular Recordings using Amortized Variational Inference

- Computer Science, BiologybioRxiv
- 2019

This work presents a Bayesian modelling approach for localizing the source of individual spikes on high-density, microelectrode arrays and demonstrates that it is more accurate than and can improve spike sorting performance over heuristic localization methods such as center of mass.

### Scalable Spike Source Localization in Extracellular Recordings using Amortized Variational Inference

- Computer Science, Biology
- 2019

This work presents a Bayesian modelling approach for localizing the source of individual spikes on high-density, microelectrode arrays and demonstrates that it is more accurate than and can improve spike sorting performance over heuristic localization methods such as center of mass.

### Inference of Multiplicative Factors Underlying Neural Variability in Calcium Imaging Data

- BiologyNeural Computation
- 2022

A flexible modeling framework is developed that identifies low-dimensional latent factors in calcium imaging data with distinct additive and multiplicative modulatory effects that govern trial-to-trial variation in evoked responses and applies it to experimental data from the zebrafish optic tectum.

### Parallel inference of hierarchical latent dynamics in two-photon calcium imaging of neuronal populations

- Computer SciencebioRxiv
- 2021

The system VaLPACa (Variational Ladders for Parallel Autoencoding of Calcium imaging data) solves the problem of disentangling deeper- and shallower-level dynamics by incorporating a ladder architecture that can infer a hierarchy of dynamical systems by incorporating sequential variational autoencoders.

### LeMoNADe: Learned Motif and Neuronal Assembly Detection in calcium imaging videos

- BiologyICLR
- 2019

This work proposes LeMoNADe, a new exploratory data analysis method that facilitates hunting for motifs in calcium imaging videos, the dominant microscopic functional imaging modality in neurophysiology.

### CALFADS: LATENT FACTOR ANALYSIS OF DYNAMI- CAL SYSTEMS IN CALCIUM IMAGING DATA

- Computer Science
- 2020

The results demonstrate that variational ladder autoencoders are a promising approach for inferring hierarchical dynamics in experimental settings where the measured variable has its own slow dynamics, such as calcium imaging data.

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