April 8, 2002 Greetings to all the Mini Analysis Program users! This newsletter informs the users of Mini Analysis Program about the updates and changes in the program. As the deadline for Society for Neuroscience Abstract submission approaches (May 6th, 2002), Mini Analysis Program is all ready for another successful year by offering many new features in the latest version of 5.5.1. With Mini Analysis Program, users can automatically detect various types of peaks, including synaptic currents or potentials, action potentials, amperometric peaks, Calcium transients, ECG peaks, POP spikes, etc. After detection of the peaks, users can perform specific analysis from a variety of choices, such as AP wave form analysis, decay fitting, cross/auto correlation, burst analysis, amperometric peak analysis, etc. The features are too many to list. If you haven't tried it, please try our full demo version avaiable at http://www.synaptosoft.com. It will make your analysis super fast! Mini Analysis Program version 5.5 is just released. To upgrade from previous versions, download the MiniAnal.exe file from our upgrade home page at http://www.syanptosoft.com/MiniAnalysis/UpgradeOnly.html. The Most exciting features in version 5.5 include the brand new Heart Rate Variability Analysis module and enhanced Action Potential Waveform Analysis. Topics; 1. Heart rate variability analysis, making it possible to analyze 24 hour ECG recordings. 2. Complete Action Potential Waveform analysis. 3. Tips on Non-stationary noise analysis. 4. Improvements for data display and other new features. 5. ABF Utility converts more files; Biopac AcqKnowledge v2 and DataQuest A.R.T. 6. New version of Channelab offers episodic data analysis. 7. Reports on the Satelite Symposium in San Diego. 8. Lab site license and registration issues. ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------- 1. Heart rate variability analysis, making it possible to analyze 24 hour ECG recordings. You might ask, "who needs Heart Rate Variability (HRV) analysis tools?" It turns out that ECG recordings share many similarities to spontaneous minis or action potential spikes. Unfortunately, people who study ECG recordings do not have access to inexpensive and easy-to-use programs that neuroscientists do enjoy with Mini Analysis Program. Several investigators have asked us to modify Mini Analysis Program to accomodate ECG recordings. The latest version 5.5.1 contains fruitful outcome of such communications with these investigators. If you have any colleagues who records and studies ECG recordings and heart rate variability, please let them know about these new additions in Mini Analysis Program. The focus of this addition has been put on the ability to detect ECG peaks from long recordings (24 hour recordings), as well as short recordings. The program can now detect ECG peaks automatically, easily calculate RR-intervals, scan and reject spurious RR-intervals, and scan and locate missing beats. After detection of ECG peaks, the program will let you plot well-know plots for HRV analysis (RR-Interval Histogram, Delta RR-Interval Histogram, Lorenz Plot and Tachogram) all at once with a simple mouse click. These are essential tools for so called geometrical HRV analysis. The program also allows you to perform comprehensive time-domain measurements of HRV based on RR-Intervals. You can divide the entire recording into many segments and analyze in short time segments as well the entire duration. The program reports more than 20 different parameters that describe the ECG recordings. These parameters include mean and standard deviation of RR-intervals, and etc (too many to list). As it is now, the program does not contain Frequency-domain measurement of HRV. And we are looking for any investigator who whould like to participate in developing this feature. If you are interested please contact us at web@synaptosoft.com. 2. Complete Action Potential Waveform analysis. We have overhauled the AP waveform analysis in Group Analysis, adding new parameters and making the exisiting algorithms much more tighter and accurate. Now AP waveform analysis measures the following parameters for each peak: amplitude, time of event, baseline, 10-90% rise, area, half-width, slope, peak (absolute value), peak to AHP 90% time, threshold, width at certain potential above baseline, AHP area, AHP peak, decay %. In previous versions, the threshold calculation was not very reliable. The program uses the peak of 3rd differential in between the time range from baseline to peak as the threshold. The inaccuracy of the threshold detection often originated from the noisiness of the 3rd differential. Therefore, in the latest version, the noise is greatly reduced by taking each differential, filtering the differentiated trace with digital gaussian filter, and smoothing the filtered trace by number of points (user can set how many points to smooth). This procedure is repeated for 1st, 2nd and 3rd differentials. After this extensive filtering and smoothing, the threshold is distinguished much better and it appears to work everytime. Due to extensive filtering and smoothing, the speed of analysis has been slowed down a little. But with a fast computer, it should not be any problem. For those who want to use the threshold as baseline, this new algorithm will be a great improvement because most of the other parameters would be heavily dependent on the threshold. The AHP (after hyperpolarization) calculation also received a special attention in this new version. Experienced users should have noticed that AHP peak and AHP area can be dependent on the number of blocks to display setting. To overcome this problem, the new version keeps track of the location of the next peak and finds the minimum point between the two consecutive peaks as the AHP. Therefore, one should display more than one peak to get the accurate measurement of the AHP and AHP are. Also, users should make sure that the peaks are sorted by time in the main window before starting the AP waveform analysis. Some users are still confused about how the program calculates the slope. The settings for slope measurement are Ym and Yt. Yt and Ym set the range of slope calculation in the rising phase of an AP. Yt sets the initial height from the baseline and Ym sets the height above Yt to calculate the slope. For example, for Yt=2 and Ym=5, the program calculates the slope starting from 2mV above baseline and ending at 5 mV above the Yt. This value is very useful for anlyzing EPSPs that preceed an action potential. There are several ways to measure the decay of an action potential. One way is to use Peak to AHP 90% time parameter. This parameter is defined as the time it takes to go from the peak to the 90% of peak to AHP peak. Another way is to use different setting for decay % measurement. The available settings are 90-50%, 90-37%, 90-20%, 90-10%, 90-0%, 80-50%, 80-37%, 80-20%, 80-10%, and 80-0%. For example, the program measures decay 90% to decay 50% of the peak to baseline for the setting of 90-50%. 3. Tips on Non-stationary noise analysis. Since the first release of non-stationary noise analysis (NSNA) module in version 5.4.1, more and more people are starting to use this feature. The basic concept behind this algorithm is that when channel has high probability of opening the variance of current trace is low and similary when channel has low probability of opteing the variance is low. The intermediate probability will give more variance. This is why the relationship between variance and amplitude is a downward parabola. It assumes that there is one conductance level. Before using this feature, it is ablsolutely necessary to understand the limitations and caveats of this analysis. It provides only an estimate of single channel parameters. These parameters should not be over interpreted. Please consult with our tech support for further instructions on how to optimally use this feature. The usage of the program is summarized as the following. Using NSNA, single channel parameters can be estimated by obtaining a variance-current relationship of noise in the decay phase of a synaptic current. By fitting the variance-current plot, one can estimate the unitary conductance, total number of channels, and probability of opening at the peak. This new feature is implemented in Group analysis and curve fitting window with an easy to use interface. After detecting and grouping the favorite synaptic currents, display the grouped events in Group Analysis window, and then press the Start button to initiate the analysis. The program will (1)display mean-difference traces, (2)display variance trace, (3)calculate variances for each amplitude bins in the decay phase of each raw trace, (4)plot the variance vs. current amplitude, and (5)fit the variance-current relationship for the best parabola, var=iI-I^2/N+Offset. These are done all automatically. The resulting fit will give the single channel parameters. The following is the list of specific suggestions for peforming NSNA on miniature EPSCs. Select "good minis" as a group in the main window. "Good minis" would be minis with no double peak or spurious noise or kink in the trace. The cleaner the selected peaks are the better results you will get. After selecting your favorite minis, sort the events by amplitude. In group analysis display the traces as scaled superimposed, baseline adjusted, and peaks aligned by rise50. Adjust the number of blocks to display, so that full decay is included in the display window. Set the number of amplitude bins, which indicates the number of vertical bins. set the number of consecutive traces to average. This parameter determines the average trace that is used for calculating mean-difference plot. This parameter is particularly useful for macroscopic currents that may display steady rundown. We recommend using 5 consecutive traces to average macroscopic currents. For spontaneous minis, this may not be as critical. Start with averaging "All traces" and try with various settings and see which gives the best smooth parabola with the least number of outliers. For example, for the setting of 5, the program will average 5 neighboring traces, centered around the current raw trace, and use this mean trace to subtract from the raw trace. The success of this analysis depends on how "nice" the resulting variance vs amplitude relationship is. The less scatter the plot and more parabolic it is, the better estimate of single channel parameters is. 4. Improvements for data display and other new features. In group analysis window, users can easily display 1st, 2nd, 3rd differentials with or without smoothing using gaussian filter and multi-point averaging. In the main window, # blocks to display setting is now allowed to be decimal number. This is particulary useful, if you have episodic traces and you want to display exactly one episode in one window. In previous versions, changing certain detection parameters forced users to reset the events. Now in the new version the need for resetting has been eliminated, allowing users to change detection parameters freely. This will make it easier to include different types of peaks detected with different sets of parameters. In the new version, users can add File Comments up to 56 characters. File comments are added or edited by a command under File menu of the main window. With data files that were recorded as Event-driven, fixed length or Event-driven, variable length mode, users can extract time information of each event called Synch Array. Synch Arrays can be directly imported into Data Array #1 or #2. Or event the interevent-intervals can be automatically calculated and imported into Data Array #1 or #2. The new command is under File menu. In the latest version, a new plot has been added. This plot is called Inverse Cumulative Histogram. It is sort of a mirror image of cumulative histogram. Users can determine the maximum amplitude in a distribution by finding the x-axis intercept on this plot. Please try it out for fun. The new plot can be generated from the Plot menu. 5. ABF Utility converts more files; Biopac AcqKnowledge v2 and DataQuest A.R.T. ABF Utility is continuously adding more file formats to be converted to ABF files. New file formats include Biopac AcqKnowledge v2 files and DataQuest A.R.T files. Please feel free to ask us if you have a file that you would like to convert to ABF file, the format that Mini Analysis Program recognizes. 6. New version of Channelab offers episodic data analysis. Channelab is an essential program for single channel kinetic modeling. It has over 75 built in various single channel models for ligand and voltage gated channels. In the recent update, Channelab improved its macroscopic analysis module. Now users of Channelab can analyze data records that are recorded in episodes or sweeps. Users can easily and automatically analyze evoked synaptic responses or macroscopic currents from excised patches or whole cell. The program will report various parameters including, amplitude, 10-90 rise, latency, half-width, area, and others. More importantly it will fit the decay to the exponential functions and report decay taus and amplitudes. This new feature in Channelab should be complementary to Mini Analysis which is useful for primarily spontaneous events. 7. Reports on the Satelite Symposium in San Diego. Synaptosft would like to thank everyone who attended the symposium at the neuroscience meeting in San Diego. We had such a great turn out with more than 60 attendees, despite the threats of national security and economic crisis after Sept 11. Perhaps in next year's symposium we will include a more informal meeting in which people can come in with specific questions and problems to discuss in a round-table format. We would like to hear your feedback on the formats of the symposium. 8. Lab site license and registration issues. Users who currently have multiple copies or who are considering getting more copies of Mini Analysis program should consider converting them to a lab site license. A lab site license entitles up to 10 copies for $1000.00. If you currently own any copies, we will deduct any previous purchases toward this amount. For example, if you previously purchased 2 copies and paid $500 then you only have to pay $500 more to convert to a lab site license. With 10 copies you should be able to supply everyone in your lab and even notebooks and home computers for a typical sized lab. As you all know, transfer of registration is free of charge. When there is a hard drive crash, reformatting of hard drive, upgrading windows, or changing of computer, one needs to transfer a registration. We strongly recommend users to download the demo program from our website, install the program on a new hard drive, and fill out the registration form either from the demo program or from our website. This way we can keep track of the registrations better. Please follow these routes when you are transferring your registration. ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------- If you haven't try the demo, please visit us at http://www.synaptosoft.com, download the demo, and try! *****Mini Analysis Program is a product of joint effort by all of the users. If you have any suggestions, please let us know, we will incorporate your ideas.****** For more information, visit our website at http://www.synaptosoft.com. If you want to receive the upgrade, please download the demo at http://www.synaptosoft.com/DownloadDemo.html. If you wish to be removed from this newsletter mailing list please mailto: Reply@synaptosoft.com. Synaptosoft Inc. 3098 Anderson Place Decature, GA 30033 phone: 770-939-4366 fax: 770-939-9473 http://www.synaptosoft.com http://www.MiniAnalysis.com http://www.PeakAnalysis.com http://www.EasyArticles.com ftp://ftp.synaptosoft.com mailto:Web@synaptosoft.com