ResearchPad - software-development https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Mechanism to prevent the abuse of IPv6 fragmentation in OpenFlow networks]]> https://www.researchpad.co/article/elastic_article_7717 OpenFlow makes a network highly flexible and fast-evolving by separating control and data planes. The control plane thus becomes responsive to changes in topology and load balancing requirements. OpenFlow also offers a new approach to handle security threats accurately and responsively. Therefore, it is used as an innovative firewall that acts as a first-hop security to protect networks against malicious users. However, the firewall provided by OpenFlow suffers from Internet protocol version 6 (IPv6) fragmentation, which can be used to bypass the OpenFlow firewall. The OpenFlow firewall cannot identify the message payload unless the switch implements IPv6 fragment reassembly. This study tests the IPv6 fragmented packets that can evade the OpenFlow firewall, and proposes a new mechanism to guard against attacks carried out by malicious users to exploit IPv6 fragmentation loophole in OpenFlow networks. The proposed mechanism is evaluated in a simulated environment by using six scenarios, and results exhibit that the proposed mechanism effectively fixes the loophole and successfully prevents the abuse of IPv6 fragmentation in OpenFlow networks.

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<![CDATA[OpenCASA: A new open-source and scalable tool for sperm quality analysis]]> https://www.researchpad.co/article/5c4b7f54d5eed0c484841137

In the field of assisted reproductive techniques (ART), computer-assisted sperm analysis (CASA) systems have proved their utility and potential for assessing sperm quality, improving the prediction of the fertility potential of a seminal dose. Although most laboratories and scientific centers use commercial systems, in the recent years certain free and open-source alternatives have emerged that can reduce the costs that research groups have to face. However, these open-source alternatives cannot analyze sperm kinetic responses to different stimuli, such as chemotaxis, thermotaxis or rheotaxis. In addition, the programs released to date have not usually been designed to encourage the scalability and the continuity of software development. We have developed an open-source CASA software, called OpenCASA, which allows users to study three classical sperm quality parameters: motility, morphometry and membrane integrity (viability) and offers the possibility of analyzing the guided movement response of spermatozoa to different stimuli (useful for chemotaxis, thermotaxis or rheotaxis studies) or different motile cells such as bacteria, using a single software. This software has been released in a Version Control System at Github. This platform will allow researchers not only to download the software but also to be involved in and contribute to further developments. Additionally, a Google group has been created to allow the research community to interact and discuss OpenCASA. For validation of the OpenCASA software, we analysed different simulated sperm populations (for chemotaxis module) and evaluated 36 ejaculates obtained from 12 fertile rams using other sperm analysis systems (for motility, membrane integrity and morphology modules). The results were compared with those obtained by Open-CASA using the Pearson’s correlation and Bland-Altman tests, obtaining a high level of correlation in all parameters and a good agreement between the different used methods and the OpenCASA. With this work, we propose an open-source project oriented to the development of a new software application for sperm quality analysis. This proposed software will use a minimally centralized infrastructure to allow the continued development of its modules by the research community.

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<![CDATA[Ten simple rules for documenting scientific software]]> https://www.researchpad.co/article/5c254517d5eed0c48442be5e ]]> <![CDATA[Towards a process management life-cycle model for graduation projects in computer engineering]]> https://www.researchpad.co/article/5c2400dfd5eed0c48409985a

Graduation projects play an important role in computer engineering careers in which students are expected to draw upon their knowledge and skills that were acquired since admission. To manage the activities of graduation projects, an iterative and incremental approach which aims continuous improvement is proposed as an alternative to a controversial delivery model. However, such integration brings up a set of challenges to be taken into account: e.g. multiple project deliveries, more labor-intensive effort from instructors, and ultimately continuous learning for all participants. One promising way to achieve such an integrated and continuous deployment velocity is to eliminate potential bottlenecks by giving student teams to receive early and continuous feedback. To this end, we propose a continuous feedback and delivery mechanism for managing the life-cycle of a graduation project through draft proposal, literature review, requirements gathering, design, implementation and testing which should produce intermediate outputs at predefined intervals. Most importantly, our approach makes it possible to quantify most of the activities involved in life-cycle process with various rubrics (i.e. measurement scales) that have been purposefully developed. The proposed model promotes the fact that all improvements should be monitored, evaluated and documented. The results of this study indicate that students who were managed using this approach produced better project deliverables and ultimately have delivered better and successful projects.

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<![CDATA[Clinical Factors Associated with Lamina Cribrosa Thickness in Patients with Glaucoma, as Measured with Swept Source Optical Coherence Tomography]]> https://www.researchpad.co/article/5989db4cab0ee8fa60bdaaa7

Purpose

To investigate the influence of various risk factors on thinning of the lamina cribrosa (LC), as measured with swept-source optical coherence tomography (SS-OCT; Topcon).

Methods

This retrospective study comprised 150 eyes of 150 patients: 22 normal subjects, 28 preperimetric glaucoma (PPG) patients, and 100 open-angle glaucoma patients. Average LC thickness was determined in a 3 x 3 mm cube scan of the optic disc, over which a 4 x 4 grid of 16 points was superimposed (interpoint distance: 175 μm), centered on the circular Bruch’s membrane opening. The borders of the LC were defined as the visible limits of the LC pores. The correlation of LC thickness with Humphrey field analyzer-measured mean deviation (MD; SITA standard 24–2), circumpapillary retinal nerve fiber layer thickness (cpRNFLT), the vertical cup-to-disc (C/D) ratio, and tissue mean blur rate (MBR) was determined with Spearman's rank correlation coefficient. The relationship of LC thickness with age, axial length, intraocular pressure (IOP), MD, the vertical C/D ratio, central corneal thickness (CCT), and tissue MBR was determined with multiple regression analysis. Average LC thickness and the correlation between LC thickness and MD were compared in patients with the glaucomatous enlargement (GE) optic disc type and those with non-GE disc types, as classified with Nicolela’s method.

Results

We found that average LC thickness in the 16 grid points was significantly associated with overall LC thickness (r = 0.77, P < 0.001). The measurement time for this area was 12.4 ± 2.4 minutes. Average LC thickness in this area had a correlation coefficient of 0.57 with cpRNFLT (P < 0.001) and 0.46 (P < 0.001) with MD. Average LC thickness differed significantly between the groups (normal: 268 ± 23 μm, PPG: 248 ± 13 μm, OAG: 233 ± 20 μm). Multiple regression analysis showed that MD (β = 0.29, P = 0.013), vertical C/D ratio (β = -0.25, P = 0.020) and tissue MBR (β = 0.20, P = 0.034) were independent variables significantly affecting LC thickness, but age, axial length, IOP, and CCT were not. LC thickness was significantly lower in the GE patients (233.9 ± 17.3 μm) than the non-GE patients (243.6 ± 19.5 μm, P = 0.040). The correlation coefficient between MD and LC thickness was 0.58 (P < 0.001) in the GE patients and 0.39 (P = 0.013) in the non-GE patients.

Conclusion

Cupping formation and tissue blood flow were independently correlated to LC thinning. Glaucoma patients with the GE disc type, who predominantly have large cupping, had lower LC thickness even with similar glaucoma severity.

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<![CDATA[A Quick Introduction to Version Control with Git and GitHub]]> https://www.researchpad.co/article/5989d9fbab0ee8fa60b722e7 ]]> <![CDATA[ReNE: A Cytoscape Plugin for Regulatory Network Enhancement]]> https://www.researchpad.co/article/5989da00ab0ee8fa60b73ae1

One of the biggest challenges in the study of biological regulatory mechanisms is the integration, americanmodeling, and analysis of the complex interactions which take place in biological networks. Despite post transcriptional regulatory elements (i.e., miRNAs) are widely investigated in current research, their usage and visualization in biological networks is very limited. Regulatory networks are commonly limited to gene entities. To integrate networks with post transcriptional regulatory data, researchers are therefore forced to manually resort to specific third party databases. In this context, we introduce ReNE, a Cytoscape 3.x plugin designed to automatically enrich a standard gene-based regulatory network with more detailed transcriptional, post transcriptional, and translational data, resulting in an enhanced network that more precisely models the actual biological regulatory mechanisms. ReNE can automatically import a network layout from the Reactome or KEGG repositories, or work with custom pathways described using a standard OWL/XML data format that the Cytoscape import procedure accepts. Moreover, ReNE allows researchers to merge multiple pathways coming from different sources. The merged network structure is normalized to guarantee a consistent and uniform description of the network nodes and edges and to enrich all integrated data with additional annotations retrieved from genome-wide databases like NCBI, thus producing a pathway fully manageable through the Cytoscape environment. The normalized network is then analyzed to include missing transcription factors, miRNAs, and proteins. The resulting enhanced network is still a fully functional Cytoscape network where each regulatory element (transcription factor, miRNA, gene, protein) and regulatory mechanism (up-regulation/down-regulation) is clearly visually identifiable, thus enabling a better visual understanding of its role and the effect in the network behavior. The enhanced network produced by ReNE is exportable in multiple formats for further analysis via third party applications. ReNE can be freely installed from the Cytoscape App Store (http://apps.cytoscape.org/apps/rene) and the full source code is freely available for download through a SVN repository accessible at http://www.sysbio.polito.it/tools_svn/BioInformatics/Rene/releases/. ReNE enhances a network by only integrating data from public repositories, without any inference or prediction. The reliability of the introduced interactions only depends on the reliability of the source data, which is out of control of ReNe developers.

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<![CDATA[Agreement between Computerized and Human Assessment of Performance on the Ruff Figural Fluency Test]]> https://www.researchpad.co/article/5989d9efab0ee8fa60b6dce4

The Ruff Figural Fluency Test (RFFT) is a sensitive test for nonverbal fluency suitable for all age groups. However, assessment of performance on the RFFT is time-consuming and may be affected by interrater differences. Therefore, we developed computer software specifically designed to analyze performance on the RFFT by automated pattern recognition. The aim of this study was to compare assessment by the new software with conventional assessment by human raters. The software was developed using data from the Lifelines Cohort Study and validated in an independent cohort of the Prevention of Renal and Vascular End Stage Disease (PREVEND) study. The total study population included 1,761 persons: 54% men; mean age (SD), 58 (10) years. All RFFT protocols were assessed by the new software and two independent human raters (criterion standard). The mean number of unique designs (SD) was 81 (29) and the median number of perseverative errors (interquartile range) was 9 (4 to 16). The intraclass correlation coefficient (ICC) between the computerized and human assessment was 0.994 (95%CI, 0.988 to 0.996; p<0.001) and 0.991 (95%CI, 0.990 to 0.991; p<0.001) for the number of unique designs and perseverative errors, respectively. The mean difference (SD) between the computerized and human assessment was -1.42 (2.78) and +0.02 (1.94) points for the number of unique designs and perseverative errors, respectively. This was comparable to the agreement between two independent human assessments: ICC, 0.995 (0.994 to 0.995; p<0.001) and 0.985 (0.982 to 0.988; p<0.001), and mean difference (SD), -0.44 (2.98) and +0.56 (2.36) points for the number of unique designs and perseverative errors, respectively. We conclude that the agreement between the computerized and human assessment was very high and comparable to the agreement between two independent human assessments. Therefore, the software is an accurate tool for the assessment of performance on the RFFT.

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<![CDATA[MuTE: A MATLAB Toolbox to Compare Established and Novel Estimators of the Multivariate Transfer Entropy]]> https://www.researchpad.co/article/5989daaaab0ee8fa60ba9208

A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different approaches to evaluate transfer entropy, some of them already proposed, some novel, and present their implementation in a freeware MATLAB toolbox. Applications to simulated and real data are presented.

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<![CDATA[Ten simple rules for making research software more robust]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf365

Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.

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<![CDATA[Implementing Spatial Segregation Measures in R]]> https://www.researchpad.co/article/5989d9f9ab0ee8fa60b7173c

Reliable and accurate estimation of residential segregation between population groups is important for understanding the extent of social cohesion and integration in our society. Although there have been considerable methodological advances in the measurement of segregation over the last several decades, the recently developed measures have not been widely used in the literature, in part due to their complex calculation. To address this problem, we have implemented several newly proposed segregation indices in R, an open source software environment for statistical computing and graphics, as a package called seg. Although there are already a few standalone applications and add-on packages that provide access to similar methods, our implementation has a number of advantages over the existing tools. First, our implementation is flexible in the sense that it provides detailed control over the calculation process with a wide range of input parameters. Most of the parameters have carefully chosen defaults, which perform acceptably in many situations, so less experienced users can also use the implemented functions without too much difficulty. Second, there is no need to export results to other software programs for further analysis. We provide coercion methods that enable the transformation of our output classes into general R classes, so the user can use thousands of standard and modern statistical techniques, which are already available in R, for the post-processing of the results. Third, our implementation does not require commercial software to operate, so it is accessible to a wider group of people.

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<![CDATA[Ten Simple Rules for Developing Public Biological Databases]]> https://www.researchpad.co/article/5989da5cab0ee8fa60b90172 ]]> <![CDATA[Practices of research data curation in institutional repositories: A qualitative view from repository staff]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbeae

The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.

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<![CDATA[Physician satisfaction with a multi-platform digital scheduling system]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdc048

Objective

Physician shift schedules are regularly created manually, using paper or a shared online spreadsheet. Mistakes are not unusual, leading to last minute scrambles to cover a shift. We developed a web-based shift scheduling system and a mobile application tool to facilitate both the monthly scheduling and shift exchanges between physicians. The primary objective was to compare physician satisfaction before and after the mobile application implementation.

Methods

Over a 9-month period, three surveys, using the 4-point Likert type scale were performed to assess the physician satisfaction. The first survey was conducted three months prior mobile application release, a second survey three months after implementation and the last survey six months after.

Results

51 (77%) of the physicians answered the baseline survey. Of those, 32 (63%) were males with a mean age of 37.8 ± 5.5 years. Prior to the mobile application implementation, 36 (70%) of the responders were using more than one method to carry out shift exchanges and only 20 (40%) were using the official department report sheet to document shift exchanges. The second and third survey were answered by 48 (73%) physicians. Forty-eight (98%) of them found the mobile application easy or very easy to install and 47 (96%) did not want to go back to the previous method. Regarding physician satisfaction, at baseline 37% of the physicians were unsatisfied or very unsatisfied with shift scheduling. After the mobile application was implementation, only 4% reported being unsatisfied (OR = 0.11, p < 0.001). The satisfaction level improved from 63% to 96% between the first and the last survey. Satisfaction levels significantly increased between the three time points (OR = 13.33, p < 0.001).

Conclusion

Our web and mobile phone-based scheduling system resulted in better physician satisfaction.

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<![CDATA[Thickness of retinal layers in the foveas of children with anisometropic amblyopia]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbf4b

Purpose

To use highly precise spectral-domain optical coherence tomography (SD-OCT) to determine whether there were structural abnormalities in the layers of different regions of the fovea in children with anisometropic amblyopia.

Methods

Eighteen children (mean age 7.8 years old; range 5–11 years) with unilateral anisometropic amblyopia and 18 age-matched control subjects participated. Foveal thickness was measured with an enhanced depth imaging system, SD-OCT and segmented into layers using custom developed software. The thickness of each layer of the fovea was compared among amblyopic eyes, fellow eyes and control eyes with optical magnification correction for axial length and statistical correction for age and sex.

Results

The total thickness and each intra-ocular layer of the central fovea were the same for each group. However, the amblyopic eyes were significantly thicker than the normal control eyes in 2 of 4 quadrants of the peripheral retina. Exploring intra-retinal layers in these two quadrants, the nasal nerve fiber layer (NFL) and inferior inner nuclear layer (INL)were significantly thicker in amblyopic eyes than in control eyes (p = 0.01 and 0.012, respectively, by ANCOVA).

Conclusion

The SD-OCT data revealed marginal differences in some foveal layers at peripheral locations and indicated that structural differences might exist between individuals with amblyopia and visually normal control subjects. However, the differences were scattered and represented no identifiable pattern. More studies with large samples and precise locations of the retinal layers must be performed to extend the present results.

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<![CDATA[Ten Simple Rules for Curating and Facilitating Small Workshops]]> https://www.researchpad.co/article/5989db40ab0ee8fa60bd69a1 ]]> <![CDATA[Real-Time Reliability Verification for UAV Flight Control System Supporting Airworthiness Certification]]> https://www.researchpad.co/article/5989da6eab0ee8fa60b93e90

In order to verify the real-time reliability of unmanned aerial vehicle (UAV) flight control system and comply with the airworthiness certification standard, we proposed a model-based integration framework for modeling and verification of time property. Combining with the advantages of MARTE, this framework uses class diagram to create the static model of software system, and utilizes state chart to create the dynamic model. In term of the defined transformation rules, the MARTE model could be transformed to formal integrated model, and the different part of the model could also be verified by using existing formal tools. For the real-time specifications of software system, we also proposed a generating algorithm for temporal logic formula, which could automatically extract real-time property from time-sensitive live sequence chart (TLSC). Finally, we modeled the simplified flight control system of UAV to check its real-time property. The results showed that the framework could be used to create the system model, as well as precisely analyze and verify the real-time reliability of UAV flight control system.

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<![CDATA[Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding]]> https://www.researchpad.co/article/5989da36ab0ee8fa60b86481

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.

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<![CDATA[Lameness Prevalence and Risk Factors in Large Dairy Farms in Upstate New York. Model Development for the Prediction of Claw Horn Disruption Lesions]]> https://www.researchpad.co/article/5989da89ab0ee8fa60b9d54c

The main objectives of this prospective cohort study were a) to describe lameness prevalence at drying off in large high producing New York State herds based on visual locomotion score (VLS) and identify potential cow and herd level risk factors, and b) to develop a model that will predict the probability of a cow developing claw horn disruption lesions (CHDL) in the subsequent lactation using cow level variables collected at drying off and/or available from farm management software. Data were collected from 23 large commercial dairy farms located in upstate New York. A total of 7,687 dry cows, that were less than 265 days in gestation, were enrolled in the study. Farms were visited between May 2012 and March 2013, and cows were assessed for body condition score (BCS) and VLS. Data on the CHDL events recorded by the farm employees were extracted from the Dairy-Comp 305 database, as well as information regarding the studied cows’ health events, milk production, and reproductive records throughout the previous and subsequent lactation period. Univariable analyses and mixed multivariable logistic regression models were used to analyse the data at the cow level. The overall average prevalence of lameness (VLS > 2) at drying off was 14%. Lactation group, previous CHDL, mature equivalent 305-d milk yield (ME305), season, BCS at drying off and sire PTA for strength were all significantly associated with lameness at the drying off (cow-level). Lameness at drying off was associated with CHDL incidence in the subsequent lactation, as well as lactation group, previous CHDL and ME305. These risk factors for CHDL in the subsequent lactation were included in our predictive model and adjusted predicted probabilities for CHDL were calculated for all studied cows. ROC analysis identified an optimum cut-off point for these probabilities and using this cut-off point we could predict CHDL incidence in the subsequent lactation with an overall specificity of 75% and sensitivity of 59%. Using this approach, we would have detected 33% of the studied population as being at risk, eventually identifying 59% of future CHDL cases. Our predictive model could help dairy producers focusing their efforts on CHDL reduction by implementing aggressive preventive measures for high risk cows.

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<![CDATA[Low-Cost Motility Tracking System (LOCOMOTIS) for Time-Lapse Microscopy Applications and Cell Visualisation]]> https://www.researchpad.co/article/5989d9fcab0ee8fa60b7259e

Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×). In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE) of 0.81±0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17±0.004 (MDA-MB-231 breast cancer cells), 1.24±0.006 (SC5 mouse Sertoli cells) and 2.21±0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers.

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