A graphical user interface to assess the neuroinflammatory response to intracortical microelectrodes

Abstract

Background: Brain-implanted devices, including intracortical microelectrodes, are used in neuroscience applications ranging from research to rehabilitation and beyond. Significant efforts are focused on developing new device designs and insertion strategies that mitigate initial trauma and subsequent neuroinflammation that occurs as a result of implantation. A frequently published metric is the neuroinflammatory response quantified as a function of distance from the interface edge, using fluorescent immunohistochemical markers. New method: Here, we sought to develop a graphical user interface software in Matlab to provide an objective, repeatable, and easy-to-use method for analyzing fluorescence immunohistochemistry images of neuroinflammation. The user interface allows for efficient batchprocessing and review of images, and incorporates zoom and contrast features to improve the accuracy of identifying the 'region of interest' (ROI). Results: The software was validated against previously published results and demonstrated equivalent scientific conclusions. Furthermore, a comparison between novice and expert users demonstrated consistency across levels of training and a rapid learning-curve. Comparison with existing method(s): Existing methods published in the intracortical microelectrode literature include a wide variety of procedures within ImageJ and Matlab. However, specific procedural details are often lacking. Conclusions: The distribution of the methodology may promote efficiency and reproducibility across the field seeking to characterize the tissue response to implanted neural interfaces. It may also serve as a template for researchers seeking to perform other types of histological quantification as a function of distance from an ROI.

The effect of a Mn(III)tetrakis(4-benzoic acid)porphyrin (MnTBAP) coating on the chronic recording performance of planar silicon intracortical microelectrode arrays

“…Holes from implantation were identified, and images were converted from native.CZI file format to 16-bit.TIFF for processing. A custom MATLAB script for analysis, called SECOND, was used where the implantation hole is outlined and any artifacts are excluded from analysis [ 57 ]. Using SECOND, each fluorescent marker was quantified in 50 μm bins expanding in a ring from the center of the identified implantation hole.…”

Antioxidant Dimethyl Fumarate Temporarily but Not Chronically Improves Intracortical Microelectrode Performance

“…A set of .PNG (Portable Network Graphics) images containing NeuN and DAPI channels were also exported from the .CZI files for neuron counting. For analysis of stain intensity, a custom MATLAB (Mathworks, Natick, MA, USA) program, SECOND, was used to outline the implant hole and mask artifacts from the subsequent analysis [63]. Using a custom Python script, the intensities of fluorescent markers for glial fibrillary acidic protein (GFAP), CD68 (Cluster of Differentiation 68), and Immunoglobulin G (IgG) in the unmasked parts of .TIFF images were quantified and binned into 50 µm intervals based on distance from the implantation site.…”

Surgical Resection Facilitates the Access of Intravenously Administered Nanoparticles to Brain Vasculature in Mice

“…Control samples (in which mice received an injection of saline instead of FNPs) were used to determine background auto uorescence, and all images were corrected to remove background by linear subtraction. A customdesigned MATLAB program [19] was used to map pixel intensity as a function of radial distance from the user-de ned resection cavity. These data were binned and averaged across images (3-4 per mouse) and mice (3-4 per group) to develop mean concentration pro les as a function of distance.…”