Igor pro 7

Manufactured by Wavemetrics

Sourced in United States

Igor Pro 7 is a data analysis and visualization software developed by Wavemetrics. It provides a wide range of tools for scientists and researchers to analyze and display their experimental data. The software supports a variety of data formats and offers a flexible programming interface for customization.

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Lab products found in correlation

Heka epc10 double amplifier, by HEKA Elektronik (6 mentions) Masslynx 4, by Waters Corporation (5 mentions) Driftscope 2, by Waters Corporation (3 mentions) Fluorolog fl 3, by Horiba (3 mentions) Ab 772206, by Avantor (3 mentions) Prism 7, by GraphPad (3 mentions) Matlab, by MathWorks (3 mentions) Pyrex melting point capillaries, by Corning (2 mentions) Clampfit 10, by Molecular Devices (2 mentions) Wga coated, by PerkinElmer (2 mentions) Ysi scintillation proximity assay beads spa, by PerkinElmer (2 mentions) Prism 9, by GraphPad (2 mentions) Synapt g2 s hdms instrument, by Waters Corporation (1 mentions) Nanoacquity system, by Waters Corporation (1 mentions) Acquity uplc m class beh c18 column, by Waters Corporation (1 mentions) Synapt g2 s, by Waters Corporation (1 mentions) Matlab r2013a, by MathWorks (1 mentions) Opterra 2 swept field confocal microscope, by Bruker (1 mentions) Perfect focus, by Nikon (1 mentions) Pclamp 10, by Molecular Devices (1 mentions)

75 protocols using igor pro 7

Measuring Cerebral Blood Flow Dynamics with SVD Analysis

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V_RBCapp was computed with the SVD method (Kleinfeld et al., 1998 (link)) over 1s long sections using LabVIEW (National Instruments, Austin, TX, United States). Measurements were then averaged over the whole recording.
For Figure 3B, data were pooled from six mice. The distribution of diameters, V_AA and V_AR for each V_scan is shown in Supplementary Figure 1. For each V_scan, the relation between V_AA and V_AR was fit using IgorPro7 (Wavemetrics, Portland, ME, United States), creating a user-defined function corresponding to Eq. 9 and optimizing the only parameter, “V_scan.” Iterative curve-fitting was performed by minimizing the value of chi-square using the Levenberg–Marquardt algorithm and the confidence interval was calculated for V_scan at p < 0.05.
For Figure 3C, data was fit using IgorPro7 (Wavemetrics, Portland, ME, United States) using linear curve-fitting.
Simulations on Figure 1B,C, 2C–E, 3B were performed using Eqs 2, 7, 7a,b, and 9 with Microsoft Excel 2010. The error made by using V_RBCapp instead of V_RBCreal was calculated as (V_RBCreal – V_RBCapp)/V_RBCreal.

Chaigneau E., Roche M, & Charpak S. (2019). Unbiased Analysis Method for Measurement of Red Blood Cell Size and Velocity With Laser Scanning Microscopy. Frontiers in Neuroscience, 13, 644.

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Statistical Analysis of Neurophysiological Data

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Data were analyzed using the following software: Axograph X, Igor Pro7 (Wave Metrics), and Python scientific development environment Spyder (libraries: Numpy, Scipy, Axographio, Stfio, Pandas, and Matplotlib). Results were expressed as average value ± standard deviation (SD). The significance of quantitative data was determined by using Student’s t test of Igor Pro7 (Wave Metrics). To avoid problems related to pseudoreplication when comparing data from rats and mice (which typically involved recordings obtained in multiple cells from the same animal), two different approaches were adopted (Eisner, 2021 (link)). First, for the large data sets presented in Figs. 1, 2, 3, 4, 5, and 9, additional analysis was performed by averaging data values obtained from the same animal and running standard Student’s t test (Table S1). For smaller data sets presented in Figs. 6 and 7, additional hierarchical analysis was performed by using GraphPad Prism 9, which considers the structure of the data (number of cells per animal), and results are presented in corresponding supplementary figures. All data for the conclusions of this study are reported in the article.

Dapino A., Davoine F, & Curti S. (2023). D-type K+ current rules the function of electrically coupled neurons in a species-specific fashion. The Journal of General Physiology, 155(9), e202313353.

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Structural Analysis of Biomolecules via TWIMS-MS

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TWIMS-MS experiments were carried out on a Waters Synapt G2-S HDMS instrument (Milford, MA, USA). All samples were introduced via nano-electrospray ionization (nESI) using a custom-built ion source interface operated in positive ion mode. The interface was designed to accommodate nESI emitters made from Pyrex melting point capillaries (Corning, NY, USA) using a vertical micropipette puller. The capillary voltage was maintained between 0.9 – 1.5 kV. Sample cone voltage and source temperature were maintained at 10 V and 80°C, respectively. TWIMS parameters were held constant for all experiments: 60 mL/min nitrogen gas flow, 40 V wave height, and 600 m/s wave velocity. The mass spectra and TWIMS arrival time distributions (ATDs) were extracted and analyzed using DriftScope 2.7 and MassLynx 4.1 (Waters), with further analysis and graphing being performed in Igor Pro 7.0 (WaveMetrics; Lake Oswego, OR, USA) and SigmaPlot 13.0 (Systat; Chicago, IL, USA).

Rister A.L., Martin T.L, & Dodds E.D. (2019). Formation of Multimeric Steroid Metal Adducts and Implications for Isomer Mixture Separation by Traveling Wave Ion Mobility Spectrometry. Journal of mass spectrometry : JMS, 54(5), 429-436.

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Liquid Chromatography-Ion Mobility Mass Spectrometry

Cited 2 times

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LC was performed on a nanoAcquity system (Waters; Milford, MA, USA). The column was an Acquity UPLC M-Class BEH C18 column, 300 μm x 150 mm (Waters). A gradient elution was performed using methanol and water with the conditions shown in Table S2–S4 in the Supplementary Material. The LC was coupled to a Waters Synapt G2-S HDMS Q-TWIMS-TOF-MS through an electrospray ionization (ESI) source with the capillary voltage maintained at 3.1 kV. The TWIMS parameters for wave height, wave velocity, and nitrogen drift gas flow were set at 40 V, 600 m/s, and 60 mL/min, respectively, as optimized in previous studies [29 (link)–31 (link)]. Data was analyzed using DriftScope 2.4 (Waters), MassLynx 4.1 (Waters), and ORIGAMI [32 ]. Further visualization was conducted Using Igor Pro 7.0 (WaveMetrics; Lake Oswego, OR, USA) and SigmaPlot 13.1 (Systat, Chicago, IL, USA).

Rister A.L, & Dodds E.D. (2019). Liquid Chromatography-Ion Mobility Spectrometry-Mass Spectrometry Analysis of Multiple Classes of Steroid Hormone Isomers in a Mixture. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 1137, 121941.

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Glycan and Peptide Fragment Analysis

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Initial data processing was conducted in MassLynx 4.1 (Waters), with further analysis conducted in IGOR Pro 7.0 (WaveMetrics, Lake Oswego, OR, USA) and SigmaPlot 13.0 (Systat, Chicago, IL, USA). Glycan fragment assignments were made in accordance with Domon / Costello nomenclature [39 ], and peptide fragment assignments were given in line with Roepstorff / Fohlmann nomenclature [40 ]. If multiple losses or combinations of cleavages could yield a given product ion mass, the ion was assigned using a general formula for the neutral loss from the precursor ion (e.g., [M - NeuAc + H]⁺). Internal fragments were assigned by combining the cleavage names for the scissions involved (e.g., [Y₀ + b₆]⁺). The symbols used in diagramming O-glycan structures followed the conventions endorsed by the Consortium for Functional Glycomics (CFG) [41 (link), 42 (link)]. Monosaccharide names were abbreviated as follows (with symbolic descriptions given in parentheses): GalNAc, N-acetylgalactosamine (yellow square); GlcNAc, N-acetylglucosamine (blue square); Gal, galactose (yellow circle); NeuAc, N-acetylneuraminic acid (purple diamond).

Kelly M.I, & Dodds E.D. (2020). Parallel Determination of Polypeptide and Oligosaccharide Connectivities by Energy-Resolved Collison-Induced Dissociation of Protonated O-Glycopeptides Derived from Nonspecific Proteolysis. Journal of the American Society for Mass Spectrometry, 31(3), 624-632.

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Collision Cross-Section Analyses of EG Isomers

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Material sources are provided in Table S1 in the Supplementary Material. In short, solutions consisting of one EG isomer or a mixture of the two were mixed with group I metal acetate salts at a concentration of 10 μM total EG to 20 μM of salt in 50% water / methanol. These solutions were then directly infused through a nano-electrospray ionization source into a Waters Synapt G2-S (Milford, MA) undergoing TWIMS separation in positive mode. The TWIMS parameters of wave height, wave velocity, and gas flow was maintained at 40 V, 600 m/s, and 60 mL/min of nitrogen, respectively. CCSs were calibrated using known drift tube values from polyalanine in nitrogen drift gas using a quadratic fit (t_d′ = aΩ’² + bΩ’ + c) [17 (link)]. CID was performed in negative ion mode in the transfer cell using argon as the collision partner at collision energies ranging from 0 V to 45 V. All analyses were performed in four replicates on different days. The peak to peak resolution was calculated based on width at half-height as shown in Equation 1:

R_{s} = \frac{2.35 Δ t}{4 w_{FWHM, avg}}

Data was analyzed and visualized through the use of Drift Scope 2.7 and MassLynx 4.0 (Waters), Igor Pro 7.0 (WaveMetrics, Lake Oswego, OR), and SigmaPlot 13.0 (Systat, Chicago, IL).

Rister A.L, & Dodds E.D. (2019). Ion Mobility Spectrometry and Tandem Mass Spectrometry Analysis of Estradiol Glucuronide Isomers. Journal of the American Society for Mass Spectrometry, 30(10), 2037-2040.

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Electrophysiology Analysis of LTD and LTP

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All off-line analyses of experimental data were carried out using IgorPro 7.0 (WaveMetrics; RRID:SCR_000325), Matlab R2013a (MathWorks; RRID:SCR_001622), and JASP (2019) version 0.9.2. The results for each experiment were obtained from at least three rats. The results were pooled and displayed as means ± SEM. The steady-state level of LTD and LTP was calculated as the average EPSP or IPSP amplitude 30 min after the depolarization protocols and was presented as the percentage of the average of the baseline (the first 5 min of baseline) EPSP or IPSP amplitude. A Mann-Whitney U test for paired experiments and F statistics for linear regression were used to test for significance in all the experiments.

Gorodetski L., Loewenstern Y., Faynveitz A., Bar-Gad I., Blackwell K.T, & Korngreen A. (2021). Endocannabinoids and Dopamine Balance Basal Ganglia Output. Frontiers in Cellular Neuroscience, 15, 639082.

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Fluorescence Recovery After Photobleaching

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FRAP experiments were performed with the Opterra II Swept Field Confocal Microscope (Bruker) using Prairie View 5.5 Software. Immediately before imaging, the medium was changed to 500 μL complete phenol red-free DMEM medium (HyClone). During imaging, cells were maintained at 37°C and supplied with 5% CO₂ using a Bold Line Cage Incubator (Okolabs) and an objective heater (Bioptechs). Imaging was performed using a 60x Plan Apo 1.40NA oil objective and Perfect Focus (Nikon) was engaged for the duration of the capture.
For imaging, cells were selected based on level of intensity. Time lapses were taken using the 488-nm imaging laser set at 100 power and 100-ms exposure with acquisition set at max speed (0.5 ms period) for 100 frames. Photobleaching of the nucleus occurred 2 s into capture, using the 488-nm FRAP laser to bleach the green channel. Data was repeated in triplicate for each condition, with each replicate having at least n = 10 cells. Data was opened in ImageJ 1.51J (NIH) using the Prairie Reader plugin. ROIs were generated in the photobleach region, a non-photobleached cell, and the background for each timelapse, and the mean intensity of each was extracted. These values were exported into Igor Pro 7.0 (WaveMetrics), where photobleach and background correction were performed, and fit FRAP curves using Hill’s equation were generated.

Batlle C., Yang P., Coughlin M., Messing J., Pesarrodona M., Szulc E., Salvatella X., Kim H.J., Taylor J.P, & Ventura S. (2020). hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation. Cell Reports, 30(4), 1117-1128.e5.

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Isolating GABA receptor currents

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To record spontaneous postsynaptic currents (sPSC), a blocking solution containing 10 µM NBQX, 50 µM D-APV and 5 µM CGP55845 was applied via the perfusion system to isolate GABA_A receptor currents. After equilibration of the blocking solution in the recording chamber, spontaneous activity was recorded for 5 min. To record miniature postsynaptic currents (mPSC), 0.5 µM TTX was added to the blocking solution. mPSCs were recorded for 5–10 min. mPSCs were identified using template-based event detection (pClamp 10.0 software; Molecular Devices, San Jose, CA, USA). Events detected by template search were controlled visually before being accepted for further analysis, which was performed with Igor Pro 7 software (WaveMetrics, Lake Oswego OR, USA). Only recordings with at least two events were accepted for further calculations. Recordings were filtered at 1 kHz and sampled at 10 kHz.

Patt L., Tascio D., Domingos C., Timmermann A., Jabs R., Henneberger C., Steinhäuser C, & Seifert G. (2023). Impact of Developmental Changes of GABAA Receptors on Interneuron-NG2 Glia Transmission in the Hippocampus. International Journal of Molecular Sciences, 24(17), 13490.

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Fluorescence Recovery After Photobleaching (FRAP) Assay

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FRAP experiments were carried out by using the same laser scanning confocal microscope mentioned in the microscopy section at 37 °C. We used a 100× oil immersion objective lens (NA 1.49, Apo SR TIRF, Nikon). A circular region of the PM (r = 10 μm) was bleached with femtosecond laser pulses (800 nm, 2920 mW, 80 MHz, Chameleon Vision-S, Coherent, USA). Fluorescence images were simultaneously recorded at 2 frames per second by using a 488 nm laser line. To eliminate the effect of natural photobleaching, the time course fluorescence intensity of the center of the bleached region was normalized to the intensity of a nonbleached region (typically bottom left of the image). Plotted fluorescence curves were then fitted with the following equation, which is based on FRAP theory.³⁷ (link)

f (t) = a + b \cdot \exp (\frac{- 2 τ_{D}}{t}) \{I_{0} (\frac{2 τ_{D}}{t}) + I_{1} (\frac{2 τ_{D}}{t})\} .

Here, f is the normalized fluorescence intensity, a and b are constants, t is time, I₀ and I₁ are modified Bessel functions, and τ_D is the fluorescence recovery time. We determined the diffusion coefficient D using

τ_{D} = w^{2} / 4 D

, where w is the radius of the bleached region. The fitting was carried out by using Igor Pro 7 software (WaveMetrics, USA). We obtained the mean values of D from more than four samples for each PM-cadDNA, PM-DNA, PM-cad, and Texas red-DHPE-labeled SOPC membrane condition.

Togo S., Sato K., Kawamura R., Kobayashi N., Noiri M., Nakabayashi S., Teramura Y, & Yoshikawa H.Y. (2020). Quantitative evaluation of the impact of artificial cell adhesion via DNA hybridization on E-cadherin-mediated cell adhesion. APL Bioengineering, 4(1), 016103.

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