Elsevier

Journal of Neuroscience Methods

Volume 155, Issue 2, 15 September 2006, Pages 172-179
Journal of Neuroscience Methods

Semi-automated quantification of axonal densities in labeled CNS tissue

https://doi.org/10.1016/j.jneumeth.2005.12.021Get rights and content

Abstract

Current techniques used to quantify axons often rely upon manual quantification or potentially expensive commercially available programs for automated quantification. We describe a computerized method for the detection and quantification of axons in the rat CNS using readily available free software. Feature J, a java-based plug-in to the imaging software NIH Image J, faithfully detects linear structures such as axons in confocal or bright-field images using a Hessian-based algorithm. We validated the method by comparing values obtained by manual and automated analyses of axons induced to grow in response to neurotrophin over-expression in the rat spinal cord. We also demonstrated that the program can be used to quantify neurotrophin-induced growth of lesioned serotonergic axons in the rat cortex, where manual measurement would be impractical due to dense axonal growth. The use of this software suite provided faster and less biased quantification of labeled axons in comparison to manual measurements at no cost.

Introduction

Imaging techniques are widely used in the field of neuroscience to visualize neuro-anatomical tracings of axonal processes. However, current analyses often rely upon manual counting, a time-intensive and tedious task, or upon potentially expensive commercially available programs (Maxwell et al., 1996) or extensive programming skills (Ponomarev and Davis, 2003). Therefore, we sought to apply a computerized method to quantify labeled axons from confocal or bright-field photomicrographs using software available in the public domain.

NIH Image J with the software plug-in Feature J (Meijering, 2003) is a less expensive alternative for computerized axonal quantification and has the advantage of being able to selectively detect linear structures in images using Hessian-based edge detection. The Hessian filter is currently applied for feature detection in medical images such as MRI and CT scans, mainly to detect line-like features such as vasculature (Chen and Amini, 2004, Sato et al., 1998), and is used to selectively detect linear structures in computer simulated images (Sato et al., 1998). In the filtering process, the software calculates the eigen values of a Hessian matrix for each pixel to describe the local second-order structure of the signal, providing both edge detection and shape information (Hladuvka and Groller, 2002). Therefore, by using Feature J to select for the smallest of the eigenvalues we limit our resulting ‘eigen image’ to a display of structures with the lowest degree of curvature (Napadow et al., 2001), such as labeled axons. Traditional edge detectors, such as in Adobe® Photoshop's ‘find edges,’ use the closely related Laplacian matrix, which is the sum of the eigenvectors. While these filters can detect edges, spatial information is lost and they are less suitable for thresholding (Hladuvka and Groller, 2002). We found that application of edge detection filters in Photoshop or MetaMorph® resulted in distortion, thickening and a halo effect on the axons in our images. In our hands the application of the Hessian filter functioned well to detect labeled axons from confocal or bright-field photomicrographs of CNS tissue, and the resulting analyses compared favorably to manual methods.

Section snippets

Animal surgeries

Experiments and care of all animals were performed in accordance with approved protocols of Baylor College of Medicine.

Corticospinal tract (CST) lesions, neuronal tracing and adenoviral vector delivery were performed as previously described (Zhou and Shine, 2003, Zhou et al., 2003). Ten days after a unilateral lesion of the CST, we labeled the CST axons on the unlesioned side with cortical injections of biotinylated dextran amine (BDA). Four days later, Adv.NT-3 was retrogradely delivered to

Comparison of computer software analyses of labeled axons

In searching for a computerized method to appropriately detect and analyze fluorescently labeled axons, we evaluated the effectiveness of three computer programs (MetaMorph, Photoshop, or Image J with the Feature J plug-in) and compared them to manual counting. The use of edge detection methods in either MetaMorph or Photoshop resulted in images of hollow axons, where the outside of the axon had a broad outline (Fig. 2C and D, arrows). In these situations, the numbers of pixels representing

Discussion

We describe a computerized method for the detection of labeled axons from photomicrographs using Hessian-based edge detection. This method worked well to detect labeled axons in both confocal and bright-field photomicrographs.

There are many techniques available to quantify axonal morphology and density from data sets derived from both in vitro and in vivo experiments. In some cases, a large or complex data set requires the use of sampling techniques that describe the characteristics of a

Acknowledgement

This work was funded by grants from the NIH, Christopher Reeve Paralysis Foundation, and Mission Connect of the TIRR Foundation.

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