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Igor pro v6

Manufactured by Wavemetrics
Sourced in United States

Igor Pro v6 is a data analysis and visualization software designed for scientific and engineering applications. It offers a comprehensive set of tools for data acquisition, analysis, and presentation. Igor Pro v6 provides a user-friendly interface and supports a wide range of data formats, enabling researchers and scientists to efficiently manage and interpret their experimental data.

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15 protocols using igor pro v6

1

Topography and Torsional Force Imaging

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The topography and the torsional-amplitude error images were first-order flattened to remove any tilt from the images using the Igor Pro v6.36 software (WaveMetrics Inc., Lake Oswego, OR, USA). In order to remove noise from the small-scale images a 3 × 2 Gauss filter was applied to all AFM images except for the ones used for the determination of the lateral invOLS (Fig. S4). For the calculation of the torsional and the lateral force images in Fig. 5 we wrote a Matlab code (MATLAB R2018a, MathWorks Inc., Natick, MA, USA) for the implementation of the Fourier method based on the script provided by Seeholzer et al.4 (link),35 (link). The calculated force images were smoothed with a Savitzky–Golay filter over nine points with a first-order polynomial.
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2

Characterizing Rheological Behavior of PolyhHb-Plasma Mixtures

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PolyhHbs were synthesized from human Hb and glutaraldehyde using our previously reported procedure [40 (link)]. Expired human plasma for viscosity analysis was generously donated by Transfusion Services, Wexner Medical Center, The Ohio State University, Columbus, Ohio. The rheology of PolyhHb plasma mixtures was measured using a DV3T-CP cone and plate Rheometer (Brookfield AMETEK, Middleboro, MA) with cone spindle CPA-40Z. PolyhHb was mixed with human plasma at 0.1, 0.2, and 0.3 PolyhHb to plasma volume fractions. For all measurements, 0.5 mL of solution was placed in the rheometer. While monitoring the shear stress, the shear rate was increased from 200 to 850 s-1 for human plasma, 1 to 400 s-1 for PolyhHb mixtures, and 1 to 100 s-1 for pure PolyhHb solutions. For all rheological measurements, the sample cup temperature was maintained at 37°C. The resulting shear stress (τ) and shear rate (γ) were then fit to the power law equation (Eq 1) in Igor Pro v. 6.36 (Wavemetrics, Lake Oswego, OR) to yield the flow consistency index (K) and the flow behavior index (nf).
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3

Modeling Reward-Based Decision Making

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Poststimulus time histograms (Fig. 2) were constructed with 5 ms bin width from 300 simulation trials and smoothed with a 40 ms box window. The curve fitting in Figs. 4F and 5 B and C was performed with the Levenberg–Marquardt least-squares method of IgorPro v6.36 (Wavemetrics, OR). The reward-firing rate function (Fig. 5B) was estimated from Eshel et al. (2 (link)), and it was fitted with the Hill equation with a coefficient of 0.5. The simulated discount values in Fig. 5C were fitted with the hyperbolic delay discount function 11+kt , where k [1/s] is the discount coefficient and t is the delay [s]. The significance of the linear fit in Fig. 4F was determined by the Levenberg–Marquardt algorithm of IgorPro.
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4

Pressure Sensor Data Acquisition

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Two USB-6356 X Series DAQs (National Instruments Corp., Austin, TX), connected through two signal conditioners (Model# 483C05, PCB Inc.) and operated via a laptop running SignalExpress 2014 (National Instruments), were used to acquire data. The system triggered off the “eye” pressure sensor of the center head. Data were collected with a 10 ms pre-trigger buffer for up to 0.5 s at a 1 MHz sample rate. Data analyses were performed using Igor Pro v6 (Wavemetrics, Inc., Lake Oswego, OR). Pressure data were scaled using the calibration sensitivities of each sensor and filtered at 100 kHz with Igor Pro's digital finite impulse response low-pass filter with a Hanning window.
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5

Lung Clearance Index Measurement Protocol

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MBW was performed using a closed-circuit Innocor system (PulmoTrace ApS, Glamsbjerg, Denmark), as previously described and detailed in the online supplemental file.10 18 (link) Detailed analysis and quality control were performed in a separate offline washout analysis package prepared in Igor Pro V.6 (Wavemetrics, Lake Oswego, Oregon, USA), as previously described.10 12 19 20 (link) Washout repeats were excluded if there was evidence of leak or a large difference between LCI or functional residual capacity (FRC) measurements (>25% from median).5 (link) Final LCI and FRC values are the average of at least two reproducible repeats. The upper limit of normal for LCI was 6.9.10 (link)
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6

Nonlinear Curve Fitting Protocol

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Data are presented as the mean ± standard error of the mean. P < .05 was used as the limit of statistical confidence. Curve fitting was performed by nonlinear least squares using Igor Pro v6 (WaveMetrics Inc, Portland, OR).
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7

Offline Analysis of Wash-in and Wash-out

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Analysis of wash-in and wash-out was performed offline using software prepared in Igor Pro v6 (Wavemetrics Inc., Lake Oswego, OR, USA) as previously described [10 ]. “Incompleteness” of wash-in was defined as the difference between inspired and expired SF6 concentrations, expressed as a percentage of the inspired SF6. During rebreathe wash-in, adjustment was made for the effects of CO2 removal on the concentration of SF6. LCI and FRC were calculated according to recent guidelines, including adjustment for re-inspired SF6, and pre- and post-capillary deadspaces (48 and 12 mL, respectively, for this adult MBW configuration) [9 (link)].
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8

Nonlinear Least Squares Curve Fitting

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Data are presented as the mean ± standard error of the mean. The limit of statistical confidence was P < .05. Curve fitting was performed by nonlinear least squares using Igor Pro v6 (Wavemetrics Inc, Tigard, OR).
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9

Data Analysis and Statistical Methods

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All data were analyzed and plotted using Igor Pro v6 (Wavemetrics, Inc.). Pooled data are presented with the mean and standard error of the mean (s.e.m.). Statistical significance was assessed with a Student’s t-test as implemented in Igor pro. Significant differences between means were considered to exist went the p value was less than 0.01.
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10

Whole-cell Patch-clamp Recordings of iPSC-derived Neurons

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Whole-cell patch-clamp recordings were performed on all four iPSC-derived neurons on DIV14, 21, 28, 35 with both differentiation protocols. Data was pooled for recordings performed over a period of two days for each time point unless specified. Experiments were performed using a HEKA EPC 10 USB amplifier Patch Master and analyzed using FitMaster v2 X 91 software (all HEKA electronics, Lambrecht, Germany), Igor Pro v6.3.7.2 (WaveMetrics, USA) and GraphPad Prism v9.3.1 (GraphPad Software, Inc., La Jolla, USA). Series resistance was compensated by 30–80%. Currents were low pass filtered at 10 kHz and sampled at 100 kHz. Leak current was subtracted using the P/4 method. The liquid junction potential was corrected for both voltage and current clamp recordings. Glass pipettes (Bio-medical Instruments, Zöllnitz, Germany) were pulled with a DMZ puller (Zeitz Instruments, Martinsried, Germany) to a resistance of 1.0 to 3.5 MΩ for voltage clamp recordings and 1.5 to 4 MΩ for current clamp recordings. All experiments were performed at room temperature.
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