Optosynth

Optosynth is a python package for generating synthetic voltage imaging ("Optopatch") data using empirical morphological reconstructions and paired electrophysiology measurements from Allen Brain single-neuron database.

Optosynth currently simulates the following aspects of voltage imaging data:

• spatial variability in expression of archaerhodopsin
• action potential dendritic backpropagation
• voltage propagation decay
• lowpass filtering of electrophysiology measurements according to the camera sampling rate
• conversion of voltage to fluorescence
• static and dynamic background fluorescence
• variability in global fluorescence intensity of individual neurons (i.e. tissue depth)
• Gaussian PSF
• Poisson-Gaussian camera noise

The synthetic data generated by Optosynth is extremely realistic and can be used for benchmarking denoising, spike detection, and segmentation pipelines.

Future plans include:

• multi-threading
• removing redundant parameters
• camera motion modeling (towards synthetic in vivo data)
• better reconstruction of soma (currently cicular -- Allen SDK only provides center coordinates and radius)
• 3D tissue/culture synthesis and 3D point spread function (currently, the reconstruction is purely 2D)

Requirements

Optosynth requires the following python modules:

• allensdk
• Pillow>7.0.0 (having the right version is extremely important -- Optosynth produces bad data with older versions of Pillow)
• boltons
• tqdm
• torch
• numpy
• scipy
• pandas

We will eventually package Optosynth into a proper python module. At the moments, the user must install the requirements manually.

Notebooks

• download_allen_data.ipynb: downloads relevant data from Allen Brain
• process_allen_morphology.ipynb: processes morphological reconstructions and generates binary masks for each neuron
• process_allen_elecrophysiology.ipynb: processes electrophysiology data, retains only square pulses, and generates a manifest of retain sweeps along with useful metadata (stimulation current, number of spikes, etc)
• optosynth_main.ipynb: generates and saves synthetic data, explores some aspect of the generated data