MEA-ToolBox: an Open Source Toolbox for Standardized Analysis of Multi-Electrode Array Data.

Functional assessment of in vitro neuronal networks-of relevance for disease modelling and drug testing-can be performed using multi-electrode array (MEA) technology. However, the handling and processing of the large amount of data typically generated in MEA experiments remains a huge hurdle for researchers. Various software packages have been developed to tackle this issue, but to date, most are either not accessible through the links provided by the authors or only tackle parts of the analysis. Here, we present ''MEA-ToolBox'', a free open-source general MEA analytical toolbox that uses a variety of literature-based algorithms to process the data, detect spikes from raw recordings, and extract information at both the single-channel and array-wide network level. MEA-ToolBox extracts information about spike trains, burst-related analysis and connectivity metrics without the need of manual intervention. MEA-ToolBox is tailored for comparing different sets of measurements and will analyze data from multiple recorded files placed in the same folder sequentially, thus considerably streamlining the analysis pipeline. MEA-ToolBox is available with a graphic user interface (GUI) thus eliminating the need for any coding expertise while offering functionality to inspect, explore and post-process the data. As proof-of-concept, MEA-ToolBox was tested on earlier-published MEA recordings from neuronal networks derived from human induced pluripotent stem cells (hiPSCs) obtained from healthy subjects and patients with neurodevelopmental disorders. Neuronal networks derived from patient's hiPSCs showed a clear phenotype compared to those from healthy subjects, demonstrating that the toolbox could extract useful parameters and assess differences between normal and diseased profiles.

CALIMA: The semi-automated open-source calcium imaging analyzer.

BACKGROUND AND OBJECTIVE: Ever since its discovery, calcium imaging has proven its worth in discovering new insights into the mechanisms of cellular communication. Yet, the analysis of the data generated by calcium imaging experiments demands a large amount of time from researchers. Tools enabling automated and semi-automated analysis are available, but often they allow automating only a part of the data analysis process. Therefore, we developed CALIMA (https://aethelraed.nl/calima), a free and open-source standalone software tool that provides an opportunity to quickly detect cells, to obtain the calcium spikes, and to determine the underlying network structure of neuronal cell cultures. METHODS: Owing to the difference of Gaussians algorithm applied for the cell detection, CALIMA is able to detect regions of interest (ROIs) quickly. The z-scoring algorithm provides a means to set the requirements for spike detection, and the neuronal connections can be reconstructed by analyzing the cross-correlation between the cellular activity. We evaluated CALIMA's reliability, speed, and functionality with a special focus on neuronal cell detection and network reconstruction. The evaluation was performed by using real-life data such as a known example dataset (cultured primary rat cortical neurons, University of Pennsylvania) and by analyzing video graphic footage of in vitro brain cell samples (SH-SY5Y neuroblastoma cultures, one sample with synchronous neuron firing). The obtained results were compared to the corresponding outcomes observed on same datasets for other similar software solutions. Moreover, we compared the results of segmentation and peak detection analysis, the ones obtained using CALIMA and those acquired manually. RESULTS: CALIMA was able to detect the cells in the cultures within seconds. The average sensitivity was 82% across the datasets checked, comparing favorably with the alternative software solutions. Using the correct parameters, CALIMA's Ca-spikes detection sensitivity reached 96%. Lastly, neuronal networks were reconstructed by combining the data on the ROI's activity and the cell's positions, finding the most likely inter-cell connections. CONCLUSIONS: We found that CALIMA proved to be a robust and fast tool to analyze the data of experiments for the digital reconstruction of the neuronal cellular network while being able to process the analysis steps with minimal user input required and in a time efficient manner.

Spatial patterning of the Notch ligand Dll4 controls endothelial sprouting in vitro.

Angiogenesis, the formation of new blood vessels, is a vital process for tissue growth and development. The Notch cell-cell signalling pathway plays an important role in endothelial cell specification during angiogenesis. Dll4 - Notch1 signalling directs endothelial cells into migrating tip or proliferating stalk cells. We used the directing properties of Dll4 to spatially control endothelial cell fate and the direction of endothelial sprouts. We created linear arrays of immobilized Dll4 using micro contact printing. HUVECs were seeded perpendicular to these Dll4 patterns using removable microfluidic channels. The Notch activating properties of surface immobilized Dll4 were confirmed by qPCR. After induction of sprouting, microscopic images of fluorescently labelled endothelial sprouts were analysed to determine the direction and the efficiency of controlled sprouting (Ecs). Directionality analysis of the sprouts showed the Dll4 pattern changes sprout direction from random to unidirectional. This was confirmed by the increase of Ecs from 54.5 ± 3.1% for the control, to an average of 84.7 ± 1.86% on the Dll4 patterned surfaces. Our data demonstrates a surface-based method to spatially pattern Dll4 to gain control over endothelial sprout location and direction. This suggests that spatial ligand patterning can be used to provide control over (neo) vascularization.

A novel method to understand tumor cell invasion: integrating extracellular matrix mimicking layers in microfluidic chips by "selective curing".

A major challenge in studying tumor cell invasion into its surrounding tissue is to identify the contribution of individual factors in the tumor microenvironment (TME) to the process. One of the important elements of the TME is the fibrous extracellular matrix (ECM) which is known to influence cancer cell invasion, but exactly how remains unclear. Therefore, there is a need for new models to unravel mechanisms behind the tumor-ECM interaction. In this article, we present a new microfabrication method, called selective curing, to integrate ECM-mimicking layers between two microfluidic channels. This method enables us to study the effect of 3D matrices with controlled architecture, beyond the conventionally used hydrogels, on cancer invasion in a controlled environment. As a proof of principle, we have integrated two electrospun Polycaprolactone (PCL) matrices with different fiber diameters in one chip. We then studied the 3D migration of MDA-MB-231 breast cancer cells into the matrices under the influence of a chemotactic gradient. The results show that neither the invasion distance nor the general cell morphology is affected significantly by the difference in fiber size of these matrices. The cells however do produce longer and more protrusions in the matrix with smaller fiber size. This microfluidic system enables us to study the influence of other factors in the TME on cancer development as well as other biological applications as it provides a controlled compartmentalized environment compatible with cell culturing.

Make it spin: individual trapping of sperm for analysis and recovery using micro-contact printing.

In this article, we describe the development of a high throughput platform to spatially manipulate viable sperm for motility measurements and recovery of the best single sperm for fertilization purposes. Micro-contact printing was used to pattern islands of adhesive proteins (fibronectin) separated by sperm repellent species (Pluronic acid F-127) on commercially available polystyrene substrates. Following washing, arrays of viable single sperm were captured onto the islands demonstrating for the first time that sperm can be trapped by micro-contact printing with patterning efficiency of 90% while retaining 100% viability. These were then subjected to motility analysis whilst remaining spatially confined to the islands. Single sperm motility was assessed (n = 37) by software analysis measuring the number of rotations per second (degrees s⁻¹). The assignment of array coordinates allows the more active single sperm to be easily identified and recovered by a simple micromanipulator pipette aspiration step with automated possibility for assisted reproductive technologies or further quality correlation analysis. Taken together, we show for the first time a technique to simultaneously screen thousands of viable single sperm for motility assessment while retaining the ability for single species recovery for enhanced fertilization purposes.