A semi-automated image analysis method to quantify neurite preference/axon guidance on a patterned substratum

From pixels to connections: exploring in vitro neuron reconstruction software for network graph generation

Digital reconstruction has been instrumental in deciphering how in vitro neuron architecture shapes information flow. Emerging approaches reconstruct neural systems as networks with the aim of understanding their organization through graph theory. Computational tools dedicated to this objective build models of nodes and edges based on key cellular features such as somata, axons, and dendrites. Fully automatic implementations of these tools are readily available, but they may also be purpose-built from specialized algorithms in the form of multi-step pipelines. Here we review software tools informing the construction of network models, spanning from noise reduction and segmentation to full network reconstruction. The scope and core specifications of each tool are explicitly defined to assist bench scientists in selecting the most suitable option for their microscopy dataset. Existing tools provide a foundation for complete network reconstruction, however more progress is needed in establishing morphological bases for directed/weighted connectivity and in software validation.

Proteoglycans: road signs for neurite outgrowth

Proteoglycans in the central nervous system play integral roles as "traffic signals" for the direction of neurite outgrowth. This attribute of proteoglycans is a major factor in regeneration of the injured central nervous system. In this review, the structures of proteoglycans and the evidence suggesting their involvement in the response following spinal cord injury are presented. The review further describes the methods routinely used to determine the effect proteoglycans have on neurite outgrowth. The effects of proteoglycans on neurite outgrowth are not completely understood as there is disagreement on what component of the molecule is interacting with growing neurites and this ambiguity is chronicled in an historical context. Finally, the most recent findings suggesting possible receptors, interactions, and sulfation patterns that may be important in eliciting the effect of proteoglycans on neurite outgrowth are discussed. A greater understanding of the proteoglycan-neurite interaction is necessary for successfully promoting regeneration in the injured central nervous system.

Student award winner in the undergraduate's degree category for the Society for Biomaterials 35th Annual Meeting, Orlando, Florida, April 13-16, 2011. Neurite growth in PEG gels: effect of mechanical stiffness and laminin concentration

Within a 3D environment, the chemical and mechanical properties of a scaffold can significantly influence nerve behavior. How these properties influence with nerve cells is important for optimizing neurite extension within a scaffold. The purpose of this study was to investigate the effect of low concentration poly(ethylene glycol) (PEG) with added laminin on 3D growth of dissociated dorsal root ganglia. Because of its high affinity for neurite adhesion and ability to promote extension, laminin was conjugated to the PEG chain, as well as mixed in the gel, at various concentrations to provide chemical cues. Gel stiffness, as determined by G*, significantly decreased with decreasing PEG concentration and with increasing laminin conjugate. Extension within the gels increased as the concentration of laminin increased with no difference between how laminin was presented (mixed or conjugated) to the cells. For example, in 3% PEG, extension increased from 92.29 ± 5.27 μm to 146.35 ± 13.12 μm as laminin conjugate concentration increased from plain to 100 μg/ml. Results indicated that the chemical properties of the scaffold influenced neurite growth more than the mechanical properties as laminin concentration had a greater impact on growth than the stiffness of the gel over the range studied. Neurite length as a function of scaffold stiffness and adhesion properties was also characterized and demonstrated a positive linear relationship between rate of neurite extension and laminin concentration. This study further demonstrates the importance of characterizing interactions between cell behavior and the chemical and mechanical environment.

Neuron tracing in perspective

The study of the structure and function of neuronal cells and networks is of crucial importance in the endeavor to understand how the brain works. A key component in this process is the extraction of neuronal morphology from microscopic imaging data. In the past four decades, many computational methods and tools have been developed for digital reconstruction of neurons from images, with limited success. As witnessed by the growing body of literature on the subject, as well as the organization of challenging competitions in the field, the quest for a robust and fully automated system of more general applicability still continues. The aim of this work, is to contribute by surveying recent developments in the field for anyone interested in taking up the challenge. Relevant aspects discussed in the article include proposed image segmentation methods, quantitative measures of neuronal morphology, currently available software tools for various related purposes, and morphology databases. (c) 2010 International Society for Advancement of Cytometry.

A rapid, quantitative method for assessing axonal extension on biomaterial platforms

Measuring outgrowth of neuronal explants is critical in evaluating the ability of a biomaterial to act as a permissive substrate for neuronal adhesion and growth. Previous methods lack the ability to quantify robust outgrowth, or lack the capacity to quantify growth on opaque substrates because they exploit the transparent nature of culture dishes to segregate neuronal processes from an image background based on color intensity. In this study, we sought to investigate the ability of opaque silica sol-gel materials to facilitate axonal outgrowth; therefore, a method was developed for quantifying outgrowth of neurites from dorsal root ganglion explants on these unique surfaces. Dorsal root ganglia were isolated from stage-nine chick embryos and cultured for 48 h on sol-gel materials presenting agarose and chitosan polysaccharides individually or in combination. Explants were then imaged, and basic image analysis software was used by three independent observers to obtain axonal length and axonal area measurements. Robust axon length and axonal spread measurements for ganglia cultured on agarose-chitosan sol-gel matrices yield an estimate of strong neural compatibility for these substrates over silica matrices presenting no polysaccharides, or silica matrices presenting chitosan or agarose individually. We suggest that this simple protocol for quantifying material biocompatibility offers an analysis strategy that can be used universally to the same end.

A Comparison of High-Content Screening versus Manual Analysis to Assay the Effects of Mesenchymal Stem Cell–Conditioned Medium on Neurite Outgrowth In Vitro

Bone marrow mesenchymal stem cells (MSCs) promote nerve growth and functional recovery in animal models of spinal cord injury (SCI) to varying levels. The authors have tested high-content screening to examine the effects of MSC-conditioned medium (MSC-CM) on neurite outgrowth from the human neuroblastoma cell line SH-SY5Y and from explants of chick dorsal root ganglia (DRG). These analyses were compared to previously published methods that involved hand-tracing individual neurites. Both methods demonstrated that MSC-CM promoted neurite outgrowth. Each showed the proportion of SH-SY5Y cells with neurites increased by ~200% in MSC-CM within 48 h, and the number of neurites/SH-SY5Y cells was significantly increased in MSC-CM compared with control medium. For high-content screening, the analysis was performed within minutes, testing multiple samples of MSC-CM and in each case measuring >15,000 SH-SY5Y cells. In contrast, the manual measurement of neurite outgrowth from >200 SH-SY5Y cells in a single sample of MSC-CM took at least 1 h. High-content analysis provided additional measures of increased neurite branching in MSC-CM compared with control medium. MSC-CM was also found to stimulate neurite outgrowth in DRG explants using either method. The application of the high-content analysis was less well optimized for measuring neurite outgrowth from DRG explants than from SH-SY5Y cells.

Evaluation of neurite outgrowth anisotropy using a novel application of circular analysis

Precise axon growth is required for making proper connections in development and after injury. One method of studying axon guidance and growth is through in vitro outgrowth assays that present controlled microenvironments. In this study, we applied circular statistical methods to evaluate directional neurite response. Visualization of data on a circular scale allows more accurate representation of the data, as neurite angles are inherently expressed on a circle. Here, the direction of neurite outgrowth from dorsal root ganglia derived neurons on different substrate types was quantitatively measured. Further, simulations of datasets with known circular parameters reflecting expected neurite angle distributions from different substrate types were also generated. Circular statistical methods were utilized and compared to linear statistical models widely used in the neuroscience literature. For small samples, Rao's spacing test showed the smallest occurrence of Type I errors (false positives) when tested against simulated uniform distributions. V-test and Rayleigh's test showed highest statistical power when tested against a unimodal distribution with known and unknown mean direction, respectively. For bimodal samples, Watson's U(2)-test showed the highest statistical power. Overall, circular statistical uniformity tests showed higher statistical power than linear non-parametric tests, particularly for small samples (n=5). Circular analysis methods represent a useful tool for evaluation of directionality of neurite outgrowth with applications including: (1) assessment of neurite outgrowth potential; (2) determination of isotropy of cellular responses to single and multiple cues and (3) determination of the relative strengths of cues present in a complex environment.

NeuronMetrics: software for semi-automated processing of cultured neuron images

Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of approximately 60 2D images is 1.0-2.5 h, from a folder of images to a table of numeric data. NeuronMetrics' output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery.

Transplantation of Fibroblasts that Overexpress Matrix Metalloproteinase-3 into the Site of Spinal Cord Injury in Rats

Growth-inhibitory chondroitin sulfate proteoglycans (CSPGs) are upregulated during glial scar formation at the site of spinal cord injury (SCI) in adult mammals. This CSPG-containing glial scar inhibits axonal regeneration. Matrix metalloproteinases (MMPs) can degrade CSPGs and other inhibitory proteins to promote neurite outgrowth. Increased MMP synthesis and secretion are observed in fibroblasts adjacent to tumor cells that express the protein EMMPRIN (Extracellular Matrix MetalloPRoteinase INducer). EMMPRIN transduction of cells provides an avenue to deliver increased levels of MMPs to the site of SCI in a sustained, localized, and moderate fashion. We explored the use of EMMPRIN-transduced cells as a mechanism to degrade CSPGs, facilitate axonal growth and improve recovery after SCI. Human dermal fibroblasts infected with a recombinant EMMPRIN adenovirus significantly increased secretion of MMP-3 compared to fibroblasts infected with a control adenovirus. Decreased CSPG immunoreactivity was observed in injured spinal cord sections when they were incubated with media from EMMPRIN-transduced fibroblasts. Conditioned media from EMMPRIN-transduced fibroblasts increased the length of neurites that were grown on a CSPG substrate. Rats that received contusive SCI and EMMPRIN-transduced fibroblast transplants demonstrated improved locomotor recovery compared to rats that received control fibroblasts, but not compared to other control groups. EMMPRIN-transplanted rats showed a significant increase in the number of retrogradely labeled cell bodies within brainstem nuclei and an increase in serotonergic fibers distal to the site of injury. EMMPRIN, and consequently MMP, delivery to the injured spinal cord may prove to be beneficial in reducing some of the physical barriers to axonal growth after SCI.

Effects of mechanical stimuli and microfiber-based substrate on neurite outgrowth and guidance

We introduced mechanical stimuli and micropatterned substrate with microfibers to investigate their effects on neurite outgrowth along with nerve growth factor in vitro. Two types of surface morphology were used: a surface that was coated by laminin alone and a surface where in microfibers was added on the laminin surface. PC-12 cells were seeded on both surface types and cultured for 2 d. The magnitudes of shear stresses ranged from 0.10 to 1.50 Pa. Two days after stimulation by shear stress, neurite outgrowth and its direction were measured by F-actin staining and digital image processing. When a shear stress of 0.50 Pa was applied, neurons were most highly aligned with microfibers. The average length of neurite outgrowth with microfibers was largest at a shear stress of 0.25 Pa. The results suggest that micropatterned fibers and fluid-induced shear stress are promising for stimulating neurite outgrowth in a desired direction.

Chondroitinase ABC combined with neural stem/progenitor cell transplantation enhances graft cell migration and outgrowth of growth-associated protein-43-positive fibers after rat spinal cord injury

We previously reported that the transplantation of neural stem/progenitor cells (NSPCs) can contribute to the repair of injured spinal cord in adult rats and monkeys. In some cases, however, most of the transplanted cells adhered to the cavity wall and failed to migrate and integrate into the host spinal cord. In this study we focused on chondroitin sulfate proteoglycan (CSPG), a known constituent of glial scars that is strongly expressed after spinal cord injury (SCI), as a putative inhibitor of NSPC migration in vivo. We hypothesized that the digestion of CSPG by chondroitinase ABC (C-ABC) might promote the migration of transplanted cells and neurite outgrowth after SCI. An in vitro study revealed that the migration of NSPC-derived cells was inhibited by CSPG and that this inhibitory effect was attenuated by C-ABC pre-treatment. Consistently, an in vivo study of C-ABC treatment combined with NSPC transplantation into injured spinal cord revealed that C-ABC pre-treatment promoted the migration of the transplanted cells, whereas CSPG-immunopositive scar tissue around the lesion cavity prevented their migration into the host spinal cord in the absence of C-ABC pre-treatment. Furthermore, this combined treatment significantly induced the outgrowth of a greater number of growth-associated protein-43-positive fibers at the lesion epicentre, compared with NSPC transplantation alone. These findings suggested that the application of C-ABC enhanced the benefits of NSPC transplantation for SCI by reducing the inhibitory effects of the glial scar, indicating that this combined treatment may be a promising strategy for the regeneration of injured spinal cord.

Automated identification of axonal growth cones in time-lapse image sequences

The isolation and purification of axon guidance molecules has enabled in vitro studies of the effects of axon guidance molecule gradients on numerous neuronal cell types. In a typical experiment, cultured neurons are exposed to a chemotactic gradient and their growth is recorded by manual identification of the axon tip position from two or more micrographs. Detailed and statistically valid quantification of axon growth requires evaluation of a large number of neurons at closely spaced time points (e.g. using a time-lapse microscopy setup). However, manual tracing becomes increasingly impractical for recording axon growth as the number of time points and/or neurons increases. We present a software tool that automatically identifies and records the axon tip position in each phase-contrast image of a time-lapse series with minimal user involvement. The software outputs several quantitative measures of axon growth, and allows users to develop custom measurements. For, example analysis of growth velocity for a dissociated E13 mouse cortical neuron revealed frequent extension and retraction events with an average growth velocity of 0.05 +/- 0.14 microm/min. Comparison of software-identified axon tip positions with manually identified axon tip positions shows that the software's performance is indistinguishable from that of skilled human users.

Quantitation of neurite growth parameters in explant cultures using a new image processing program

An interactive image processing program was developed to quantify the effects of various biochemical and physical factors on cultured explants of nerve tissue. We used this method to obtain a growth curve of chick embryo dorsal root ganglia (DRG) in media containing various concentrations of nerve growth factor (NGF). In the past, neurite lengths and numbers were measured manually using collages of 35 mm color photographs or made directly under the microscope. Our new program makes it possible to quantify the growth of whole live, unstained DRG's on photograph collages or digital images with respect to center area, neurite area, total explant area, and the number and length of neurites almost exclusive of background artifacts. After comparing the old and new methods, we conclude that our analysis algorithm correlates well with previously accepted protocols for assessing stimulation and inhibition of growth. It rapidly measures several biologically-relevant properties and provides a means to obtain information on six parameters (neurite area, neurite length, neurite number, center area, total area, neurite density) using a single quantitative method. Neurite area in the presence of 10 ng/ml or 20 ng/ml NGF was the most significantly increased parameter as was expected from previous studies since it includes both neurite length and number as well as any crossing fibers.

Microglia enhance dorsal root ganglion outgrowth in Schwann cell cultures

Transplantation of cellular populations to facilitate regrowth of damaged axons is a common experimental therapy for spinal cord injury. Schwann cells (SC) or microglia grafted into injury sites can promote axonal regrowth of central projections of dorsal root ganglion (DRG) sensory neurons. We sought to determine whether the addition of microglia or microglia-derived secretory products alters DRG axon regrowth upon cultures of SC. Rat DRG explants were grown on monolayers consisting of either SC, microglia, SC exposed to microglia-conditioned medium (MCM), or co-cultures with different relative concentrations of microglia. Image analysis revealed that, compared to SC alone, the extent of neurite outgrowth was significantly greater on SC-microglia co-cultures. Immunocytochemistry for extracellular matrix molecules showed that microglial cells stained positively for growth-promoting thrombospondin, whereas laminin and the inhibitory chondroitin sulfate proteoglycans (CSPGs) were localized primarily to SC. Notably, immunoreactivity for CSPGs appeared reduced in areas associated with DRG outgrowth in co-cultures and SC exposed to MCM. These results show that microglia or their secreted products can augment SC-mediated DRG regrowth in vitro, indicating that co-grafting SC with microglia provides a novel approach to augment sensory fiber regeneration after spinal cord injury.