Software | Data Analysis

Reconstruct is a Windows application for montaging, aligning, tracing, measuring, and reconstructing objects from serial section images.

License (GPL, MIT, etc): Permission to use, copy, and redistribute Reconstruct is granted without fee under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.

Platform (Programming Language, Database compatibility, etc): Microsoft Windows (XP/Vista/7/8/10)

File Formats Supported: Tiffs, jpegs, bmps

Release Schedule: Always available

Datasets available at SynapseWeb. 

See Software Page

Balanced Network
Software | Modeling

Software repository

Simulation of a plastic balanced network.

The code to run a simulation of this balanced network is composed of 4 different scripts and one function. The main code that runs the simulation is BalancedNetworkMain.m. Here is where the time of the run is determined, a long with individual neuron parameters, and the number of neurons in the network. Additionally, here is where plots such as the rasterplot, and time-dependent firign rates are generated. Lastly, this script also includes the computation of mean field spike count covariances and correlations. The spike count covariances are computed using the function SpikeCountCov.m, which calculates the spike count covariances by counting spikes over some time interval (T1 to T2) with some window size, and for each neuron. The covariances are finally obtained by taking the covariance of the matrix of spike counts.

A key component that determines the dynamics of the network is the choice of connectivity matrix. This can be adjusted at Connectivity.m, and currently the matrix is sparse and it is built with mean connection strengths between cell pairs of each type and scaled by $$1/sqrt{N}$$.

The script named ExternalLayer.m determines the structure of the external feedforward layer, which in this case it is a network of Poisson neurons with pairwise correlation 'c'.

The actual run of the network takes place in Simulation.m. In this script, we first define variables to record from some neurons and we preallocate memory. The for loop goes through each time step of the simulation and starts by propagating the feedforward spikes onto the recurrent network. Euler's method on the EIF differential equation is used to solve for the voltage at each point in time. Next, spikes are recorded into the matrix 's', whose first row stores spike times, and its second row, the neuron index. Synaptic currents are also updated using Euler's method and are recorded.

The simulation can actually run using different models. For example, if we use Simulation_AdEx.m on the main script, then each neuron will be modeled by the Adaptive EIF, instead of just the EIF formalism. This script contains only three extra parameters that control adaptation (a, b, and tauw), and it creates a figure that shows the evolution of the adaptation current over time.

Nanofractal Electrode Coating
Instrumentation | Recording

Instrument Type(s) (it can fall under multiple categories and subcategories)
Electrodeposited platinum iridium nanofractal coating for improved electrode efficiency, reduced impedance, and increased robustness

Make and Model of the Equipment

Description of what it is used for
PtIr nanofractal coatings can be deposited on 3D microelectrodes to reduce electrode impedance and increase microstimuliation capacity. 

Description of its capabilities
Thin-films that are not capable of supporting long-term electrical stimulation, due to poor robustness, can be coated with PtIr films to significantly increase the longevity for microstimulation applications. 1 kHz impedance can be reduced by 2 orders of magnitude vs. an uncoated electrode. The films are mechanical robust and withstand repeated insertion into brain.

Location (Research Facility)
PtIr coating samples can be obtained by providing MINT with a device to be coated. Coating is done at either Platinum Group Coatings (industry partner) or at MINT (starting Fall 2018).

Link to a User Manual

Other relevant documents related to the equipment

Type of research that was enhanced by its use
Long-term recording of action potentials (more spikes/channel) [1], more efficient pulse delivery with cochlear implant electrodes [2], reduced electrode impedance for cardiac electrotherapy [3]
[1] Isaac R. Cassar, Artin Petrossians, John J. Whalen, Curtis D. Lee, Jason Sharkey, Chunxiu Yu, and Warren M. Grill, Electrodeposited Platinum-Iridium Coating (EPIC) Improves In-Vivo Chronic Recording Performance of Microwire Electrode Arrays (MEA), SfN 2017

[2] Curtis D. Lee, Eric M. Hudak, John J. Whalen III, Artin Petrossians, and James D. Weiland, Low-Impedance, High Surface Area Pt-Ir Electrodeposited on Cochlear Implant Electrodes. J.. Electrochem. Soc. 2018 volume 165, issue 12, G3015-G3017

[3] Xu, Lizhi, Sarah R. Gutbrod, Yinji Ma, Artin Petrossians, Yuhao Liu, R. Chad Webb, Jonathan A. Fan et al. "Materials and fractal designs for 3D multifunctional integumentary membranes with capabilities in cardiac electrotherapy." Advanced materials 27, no. 10 (2015): 1731-1737