Axis software

Manufactured by Axion Biosystems

Sourced in United States

The AxIS software is a data acquisition and analysis platform designed for use with Axion Biosystems' product lines. It provides the core functionality for recording, visualizing, and analyzing electrophysiological data from various cell-based and tissue-based assays.

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26 protocols using axis software

Neurotoxicity Screening with MEA Data

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Raw MEA data [*.raw files generated via the Maestro system and AxIS software (Axion Biosystems), see above] from previous studies^{21 (link),22 (link)} was processed through the same analysis pipeline described above. Additional processing for neurotoxicity data was based on methods described by Shafer et al.^{21 (link)}, including area under curve (AUC) calculation, Hill function fitting, and EC₅₀ extrapolation. Specifically, AUC values for each compound and concentration were calculated in Python 3 using the trapezoidal rule (numpy.trapz() function) to integrate normalized NAS values over time (see Data Availability below for more information about custom Python codes). Concentration–response curves (NAS AUC vs. concentration) were generated via nonlinear least squares regression ([Inhibitor] vs. normalized response model) in GraphPad Prism 8.2.0 (GraphPad Software Inc., San Diego, CA) for each compound with Hill slope = − 1.0, and EC₅₀ values were extrapolated from the resulting curves.
EC₅₀ values corresponding to cytotoxicity (Supplementary Table S2) that were used for sensitivity analysis were reported from previous studies^{21 (link),22 (link)}. EC₅₀ values for NAS and average MEA parameter were calculated as described above.

Passaro A.P., Aydin O., Saif M.T, & Stice S.L. (2021). Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays. Scientific Reports, 11, 9110.

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Multielectrode Array Analysis of Hippocampal Neurons

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Each well of a 12-well MEA plate from Axion Biosystems was coated with poly-D-lysine prior to cell seeding. Hippocampal neurons from Non-Tg and hgFUS^R521H mice embryos were plated at the same density (40,000 neurons per well), with duplicate wells for each embryo. Cells were fed every 3-4 days and measurements were taken before the medium was changed. Recordings were performed using a Maestro MEA system and AxIS software (Axion Biosystems), using a band-pass filter with 0.1 Hz and 5 kHz frequency cutoffs. Spike detection was performed using the neural Spikes analog setting (1200XGain, 200-5000Hz) and an adaptive threshold set to 5.5 times the standard deviation of the estimated noise on each electrode. Each plate first rested for 5 min in the Maestro, and then 5 min of data were recorded to calculate the spike rate per well. MEA analysis was performed using the Axion Biosystems Neural Metrics Tool, wherein electrodes that detected at least 5 spikes/minute were classified as active electrodes. Bursts were identified in the data recorded from each individual electrode using an adaptive threshold algorithm. Network bursts were identified for each well requiring a minimum of ten spikes with a maximum inter-spike of 100 ms. Only channels that exhibited bursting activity (more than 10 spikes in 5-min interval) were included in the analysis.

López-Erauskin J., Tadokoro T., Baughn M.W., Myers B., McAlonis-Downes M., Chillon-Marinas C., Asiaban J.N., Artates J., Bui A.T., Vetto A.P., Lee S.K., Le A.V., Sun Y., Jambeau M., Boubaker J., Swing D., Qiu J., Hicks G.G., Ouyang Z., Fu X.D., Tessarollo L., Ling S.C., Parone P.A., Shaw C.E., Marsala M., Lagier-Tourenne C., Cleveland D.W, & Da Cruz S. (2018). ALS/FTD-Linked Mutation in FUS Suppresses Intra-axonal Protein Synthesis and Drives Disease Without Nuclear Loss-of-Function of FUS. Neuron, 100(4), 816-830.e7.

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Multielectrode Array Analysis of Mouse Neurons

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Cytoview MEA 48-well black plates (Axion, M768-tMEA-48B-5) were pre-coated with poly-L-lysine and laminin as described in the culture vessel reagent preparation section. Cortices and hippocampi were isolated and dissociated, and neurons were enriched as described above from 6-week-old mice. Cells were plated at a density of 1.2 × 10⁵ cells per well according to Axion cell culture protocol and maintained at 37°C with 5% CO₂. Recordings were performed in a Maestro MEA system and AxIS software (Axion Biosystems) using a bandwidth with a filter for 10 Hz to 2.5 kHz cutoff frequencies. Spike detection was performed using an adaptive threshold set to 5.5 times the standard deviation of the estimated noise on each electrode. Each plate rested for 10 min for acclimatization in the Maestro instrument and was then recorded for an additional 10 min to calculate spike rates. Multi-electrode data analysis was performed using the Axion Biosystems Neural Metrics Tool. An active electrode was considered once five spikes occurred over the length of 1 min (five spikes/min). Bursts were identified in the data recorded from each individual electrode using an adaptive Poisson surprise algorithm. Network bursts were identified for each well using a non-adaptive algorithm requiring a minimum of 10 spikes with a maximum inter-spike interval of 100 ms.

van Niekerk E.A., Kawaguchi R., Marques de Freria C., Groeniger K., Marchetto M.C., Dupraz S., Bradke F., Geschwind D.H., Gage F.H, & Tuszynski M.H. (2022). Methods for culturing adult CNS neurons reveal a CNS conditioning effect. Cell Reports Methods, 2(7), 100255.

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Analyzing Neuronal Spiking Activity in MEA Recordings

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Mean firing rates were calculated using AxIs software (Axion Biosystems). MEA records the extracellular spiking activity of neurons. Spikes were detected online by AxIS spike detector software as described previously (McConnell et al., 2012 (link)) and were defined as an event with amplitude >6 standard deviations (SD) above background noise. Single-electrode bursts were defined as at least five consecutive spikes with an interspike interval <100 ms. Following recording, spike sorting was performed using the AxISmetrics plotting tool (Axion Biosystems). Raster plots with histograms were plotted with NeuralMetric Tools. Raw data scatter plot and percentage change analysis was performed with custom built program in MATLAB using mean firing rate information extracted from raw data from AxIS. In the analysis of drug effect graph, after excluding inactive electrodes (<5 spikes/s), all data from electrodes from the six-well replicates of a condition was pooled together. Electrodes with firing frequency that fell in-between 25th and 75th percentile in the baseline reading before drug application were used for analysing effects post drug-addition.

Pettingill P., Weir G.A., Wei T., Wu Y., Flower G., Lalic T., Handel A., Duggal G., Chintawar S., Cheung J., Arunasalam K., Couper E., Haupt L.M., Griffiths L.R., Bassett A., Cowley S.A, & Cader M.Z. (2019). A causal role for TRESK loss of function in migraine mechanisms. Brain, 142(12), 3852-3867.

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Cardiomyocyte Electrophysiological Recording

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Electrophysiological recording of spontaneously beating cardiomyocytes was collected for 2 min using the AxIS software (Axion Biosystems). After raw data collection, the signal was filtered using a Butterworth band-pass filter and a 90μV spike detection threshold. Field potential duration was automatically determined using a polynomial fit T-wave detected algorithm.

Miklas J.W., Clark E., Levy S., Detraux D., Leonard A., Beussman K., Showalter M.R., Smith A.T., Hofsteen P., Yang X., Macadangdang J., Manninen T., Raftery D., Madan A., Suomalainen A., Kim D.H., Murry C.E., Fiehn O., Sniadecki N.J., Wang Y, & Ruohola-Baker H. (2019). TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes. Nature Communications, 10, 4671.

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Assessing Cortical Neuron Network Activity

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Neuronal network activity was recorded with an Axion Maestro system controlled by AxIS Software (Axion Biosystems, Atlanta, GA, USA) with 12.5 kHz sampling rate as described previously^{66 (link)}. The hPSC-derived cortical neurons (in-house-derived hESC line Regea 08/023 or commercial hiPSC-derived neurons, ax0018) were plated on CytoView MEA 48 plates with 16 electrodes per array. Recordings were obtained under a controlled temperature of 37 °C. Spontaneous activity development was examined once a week with 10-minute recordings. After five weeks, when synchronous network activity had developed, the experiments with astrocyte conditioned medium (ACM) were initiated. The responses to control medium, control ACM or reactive ACM were measured for 10 min immediately and at 1 h, 4 h and 24 h after application. Analysis methods for spike and burst detection are described in the Supplementary methods section.

Hyvärinen T., Hagman S., Ristola M., Sukki L., Veijula K., Kreutzer J., Kallio P, & Narkilahti S. (2019). Co-stimulation with IL-1β and TNF-α induces an inflammatory reactive astrocyte phenotype with neurosupportive characteristics in a human pluripotent stem cell model system. Scientific Reports, 9, 16944.

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Spontaneous Neuronal Activity Monitoring

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Twelve-well MEA plates (Axion Biosystems) were used and each well contained an 8 × 8 grid of 30 nm circular nanoporous platinum electrodes. Wells were coated with PDL and laminin and neurons were plated at a density of 500,000 neurons/well. MEA plates with neurons were cultured at 37°C and 5% CO₂, and cells were fed every week by neuronal differentiation media (BrainPhys Neuronal Medium N2-A & SM1 kit (STEMCELL), 2 mM L-glutamine, B27, 1 μM cAMP, 200 ng/ml L-Ascorbic Acid, 10 ng/ml BDNF and 10 ng/ml GDNF). Extracellular recordings of spontaneous action potentials were performed in culture medium at 37°C using a Maestro MEA system and AxIS software (Axion Biosystems). Data were sampled at the rate of 12.5 kHz with a hardware frequency bandwidth of 200-5000 Hz. For spike detection, the threshold was set to 6 times the rolling standard deviation of the filtered field potential on each electrode. Five-minute recordings were used to calculate average spike rate and the number of active electrodes in each well. An active electrode was defined as spike rates ≥ 0.5/min.

Wang X., Ye F., Wen Z., Guo Z., Yu C., Huang W.K., Ringeling F.R., Su Y., Zheng W., Zhou G., Christian K.M., Song H., Zhang M, & Ming G.L. (2019). Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders. Molecular psychiatry, 26(4), 1346-1360.

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Neuronal Activity Characterization via MEA

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NPCs of each line were plated at a density of 10,000 cells/well in six wells of a 96-well multielectrode array activity (MEA) plate coated with poly-l-ornithine and laminin for neuronal differentiation as described before [16 (link)]. Recordings were performed in a Maestro MEA system and AxIS software (Axion Biosystems) using a bandwidth with a filter for 200 Hz to 3 kHz cutoff frequencies. Spike detection was performed using an adaptive threshold set to 5.5 times the standard deviation of the estimated noise on each electrode. Each plate was acclimatized for 10 min in the Maestro Instrument and recorded for 10 min for quantification. Recordings were performed before media change. Multi-electrode data analysis was performed using the Axion Biosystems Neural Metrics Tool and the mean spontaneous neuronal bursts (spontaneous neuronal activity) value was determined in each well. Averages of wells with at least one active electrode were considered for the analysis presented per each cell line. An electrode was considered active at a threshold of five spikes/min. An average of 14–16 electrodes were active per line, with some variations. Only the wells that exhibited activity were included in the analysis. Neuronal firing synchrony per well was not evaluated for these experiments.

Linker S.B., Mendes A.P, & Marchetto M.C. (2020). IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism. Molecular Autism, 11, 55.

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Extracellular Recordings of Neural Network Activity

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NPCs (15,000 cells) were plated in 96-well MEA plates coated with poly-O and laminin for neuronal differentiation as described before. Extracellular recordings were performed in a Maestro MEA system and AxIS software (Axion Biosystems) using a bandwidth with a filter for 200 Hz to 3 kHz cutoff frequencies. Spike detection was performed using an adaptive threshold set to 5.5 times the standard deviation of the estimated noise on each electrode. Each plate was acclimatized for 10 min in the Maestro Instrument and recorded for 10 min for quantification. Recordings were performed before media change. When drugs were added to the media, recordings were performed just before media change and drug treatment (1 mM LiCl or 1 mM VPA). Multi-electrode data analysis was performed using the Axion Biosystems Neural Metrics Tool. An electrode was considered active at a threshold of 5 spikes/min. Each experiment was repeated 3 times with 8 or 12 replicates per plate; replicates were averaged for each cell line.

Santos R., Linker S.B., Stern S., Mendes A.P., Shokhirev M.N., Erikson G., Randolph-Moore L., Racha V., Kim Y., Kelsoe J.R., Bang A.G., Alda M., Marchetto M.C, & Gage F.H. (2021). Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients. Molecular psychiatry, 26(6), 2440-2456.

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Electrophysiological Profiling of Neuron-Astrocyte Co-Cultures

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WT and mutant hiPSC-derived NPCs (DIV 30) were co-cultured with hiPSC-derived WT astrocytes (DIV 60+) in 1:1 ratio and plated onto 48-well multielectrode array (MEA) plates (Axion BioSystems) coated with PLO/L. Cells were plated using drop seed method, where 15 μL of mixed cell suspension (60,000 cells in total) in a 10% dilution of matrigel in BrainPhys™ + 1X CultureOne™ media was pipetted onto the electrode array in the center of each well. The cultures were fed by partial media replacement every 3 days according to our neuronal differentiation protocol stated above. Spontaneous electrophysiological activity of the neuron-astrocyte co-cultures was recorded for 10 min at cortical neuron DIV 50 using the Axion biosystems maestro MEA at 37 °C and 5% CO₂. Data analysis was performed using AxIs software (Axion BioSystems) to extract the number of spikes and bursts from the recording file. Quality criteria for the assays were defined as follows: an electrode having an average of more than 5 spikes/min and wells with less than 30% of the total electrodes active were considered inactive and excluded from the analysis.

Frew J., Baradaran-Heravi A., Balgi A.D., Wu X., Yan T.D., Arns S., Shidmoossavee F.S., Tan J., Jaquith J.B., Jansen-West K.R., Lynn F.C., Gao F.B., Petrucelli L., Feldman H.H., Mackenzie I.R., Roberge M, & Nygaard H.B. (2020). Premature termination codon readthrough upregulates progranulin expression and improves lysosomal function in preclinical models of GRN deficiency. Molecular Neurodegeneration, 15, 21.

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