July 1, 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. Mini Analysis Program takes another quantum leap to include population spike/field EPSP analysis and multi peak analysis tools in the latest version 5.6.3. With these new tools, the program is equipped to analyze not only spontaneous activities that are recorded continuously but also episodic events that are recorded as periodic sweeps. This advance will open up doors for those who study LTP/LTD and epilepsy to use Mini Analysis Program for their analysis. Mini Analysis Program version 5.6 is just released. To upgrade from previous versions, download the MiniAnal.exe file from our upgrade home page at http://www.synaptosoft.com/MiniAnalysis/UpgradeOnly.html. The Most exciting features in version 5.6 include the brand new field EPSP Analysis and Multi Peak Analysis modules. Topics; 1. Opening and displaying episodic recordings 2. Multi peak analysis 3. Field EPSP and population spike analysis 4. Enhanced non-stationary analysis 5. ABF Utility converts John Dempster's WinWCP files and Spike2 multiple channel files 6. Other minor bug fixes. 7. Lab site license and registration issues. ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------- 1. Opening and displaying episodic recordings Mini Analysis was originally developed for the analysis of spontaneous activities. The demand has grown for analysis tools for episodic recordings, such as evoked synaptic responses. Mini Analysis was capable of opening these episodic files but the files were only displayed as continuous records, and the timing of each episode was lost. In version 5.6, users can open and display these episodic files as not continuous but as individual sweeps in the Group Analysis. To display episodic records, you simply open the file in the main window and then go to Group Analysis window (shortcut key, F3) to click on "Episodes" option on top of Display Tab. Once sweeps are displayed you can adjust number of blocks to display and other display options to optimize the display. This feature allows users to analyze episodic records in Group Analysis without going through detection and grouping in the main window, making Mini Analysis suitable for analysis of not only spontaneous activities but also episodic events. 2. Multi peak analysis One investigator challenged me to analyze his compound action potential and fiber volley traces, recorded from dorsal root fibers extracellularly. These traces contain multiple upward and downward peaks superimposed together, each peak representing one population of fibers with certain conduction velocity characteristics. Dorsal roots contain at least three populations of fibers with different conduction velocities. To efficiently analyze these traces, I have added the Multi Peak analysis module in Group Analysis window. It first calculates the first differential of raw trace, smoothes the differential trace with gaussian filter and 5 point average smoothing, and then looks for location of peaks where the first differential is zero. The program reports the y-value and time of each peak, up to 9 peaks. The peaks are graphically displayed as red X's and the number of peaks. In case too many peaks are detected, change the setting, "Number of points to avoid duplicate peak" to higher number. This setting lets users to avoid closely spaced peaks. An example of this analysis is shown in the Gallery section of the Mini Analysis home page at http://www.synaptosoft.com/MiniAnalysis/Gallery.html. Users can display entire file as superimposed and detect the peaks for every trace. Once all the traces are analyzed, users can easily plot the amplitudes as a time course plot or export the result spreadsheet to other programs to manipulate the results. 3. Field EPSP and population spike analysis An easy-to-use analysis tool for LTP/LTD type of experiment has been long due. Most investigators have been relying on homemade programs or old DOS programs. I have recently been exposed to field EPSP recordings myself. Thus the arrival of fEPSP/population spike analysis module was naturally initiated. The new analysis module is fully tested and confirmed of its usefulness and easiness by several experts in the field. Let us know if you have any suggestions for improvements. The following is a step-by-step procedure; - Open data file in the main window. - Open Group Analysis window (shortcut key, F3) - Display as episodes and adjust the display settings (gain, number of display blocks, baseline adjustment, etc) - Go to fEPSP tab and place the two cursors before and after a peak of interest. - Setup the analysis by clicking on various options for detecting pop spike and paired-pulse. - Press Analyze button to start the analysis. - Generate a Time Course plot under Plot menu. The module measures peak amplitude, latency, baseline, coastline, slope, area, and half-width for individual peak. When "detect population spike" option is turned on, it will report pop spike amplitude as amplitude as well as for other parameters. When paired-pulse option is turned on, it will report these parameters for two peaks along with the paired-pulse ratio values. Coastline is a measure of fluctuations in y-values and simply defined as sum of all y-values (baseline subtracted) between the two cursors. This measure can be useful for monitoring epileptic discharges in which peaks are not very well defined. Detection of peak is closely coupled to the detection parameters in the main window. The direction of peak, and "number of points to average for peak" are set in the main window. The slope calculation is quite flexible. Users can choose between different options for slope calculation. These include 10-90% rise linear regression, 20-80% rise linear regression, 50% 5 points linear regression, and steepest 1-point slope. For 10-90% rise option, the program first finds 10 and 90% rise and then finds the slope by using linear regression of all points in between 10 and 90% rise. For 50% slope, it first finds the 50% rise and then uses 5 points around 50% rise for linear regression. The steepest slope is an instantaneous slope at the steepest point, measured from the filtered and smoothed first differential trace. Detection of population spike is achieved by using the same peak detection algorithm as in Multi peak detection, namely from the gaussian-filtered and smoothed first differential trace. The amplitude of population spike is measured from the population spike peak to the intersection with a tangent line drawn between the pre- to the post-population spike peak. The three peaks, population spike peak, pre- and post-population spike peaks are graphically designated as peak A, B, and C, with a tangent line drawn between peak A and C. An example of this analysis is shown in the Gallery section of the Mini Analysis home page at http://www.synaptosoft.com/MiniAnalysis/Gallery.html. If the program misreports the location of the three peaks, users can select the appropriate peaks by clicking on Manual Detection option in the population spike analysis options. When Manual Detection is clicked, the program finds the possible peaks in the trace and put the number of peaks on the trace. Users then select the number of peak for peak A, B, and C. This forces the program to use the selected peaks for detection of population spike. If you happen to have some data with population spikes, please try this out. It is quite amusing to see how the program does this automatically and also manually with users help. The latency calculation is also quite flexible. Users can enter the time of stimulus and the program will use this time to subtract from the time of peak to calculate latency of peak from the time of stimulus. Paired-pulse ratio calculation is turned on by clicking on the option, Calculate Paired-pulse ratio. Paired-pulse ratio is determined after two peaks are analyzed by two rounds of detection routine. Pulse Interval between two consecutive stimuli determines how many points the program shifts to right for the second round of detection. Users can conveniently set the type of parameter (slope, amplitude, latency, etc) to use for ratio calculation. Once peaks are detected, users can plot the results as time course plot, a familiar scatter plot that you often see in LTP/LTD papers with normalized amplitude on y-axis and time or sweep number on x-axis. When you click the command under Plot menu of Group Analysis window, the program will ask for number of initial values to average and use for normalization. Next thing you will see is a normalized time course scatter plot. Enjoy these new features and please let us hear how you like them. 4. Enhanced non-stationary analysis In version 5.6, non-stationary noise analysis (NSNA) has added some new features for better and easier analysis. Most importantly, NSNA for synaptic currents can be achieved by simply setting the analysis type to "Synaptic Currents". This option distinguishes from the analysis type of "Macroscopic Currents" by the way average trace is obtained before each raw trace is subtracted with the average trace to obtain difference trace. With Synaptic Currents option, an ensemble trace is obtained from all of scaled raw traces, and then for each raw trace the ensemble average trace is scaled to the peak of raw trace. The difference trace is obtained by subtracting this peak scaled ensemble average trace from the raw trace. For Macroscopic Currents option, rolling averaging scheme is used. If this sounds too confusing, please contact us and we will give you more detailed info. The results of NSNA are now displayed in the results spreadsheet for better export and plotting feature. Also, the R^2 value (goodness of fit) for each parabolic fitting is fixed. Copying variance-amplitude is fixed. Users can easily copy the graph values by running "Copy Variance-Mean Plot data" command under Results menu of the Group Analysis window. Users can also access Graph Control window by clicking right button on the plot. 5. ABF Utility converts John Dempster's WinWCP files and Spike2 multiple channel files ABF Utility now supports conversion of John Dempster's WinWCP files. WinWCP files are episodic recordings and ABF Utility appropriately converts as episodic ABF files. Spike2 files that contain multiple channel recordings can be safely converted in ABF Utility. 6. Other minor bug fixes. There has been a lot of problems for some Clampfit saved files. When Clampfit saves file after filtering or other file manipulations, it rescales the original file in attempt to maximize the digitization. This created scaling problem in Mini Analysis program. In addition, files that contain Autosample additional gain also caused scale problem. In version 5.6 this problem has been fixed. If you have been encountering scaling problem, please try this new upgrade. Display of decimal block size has been reworked out after several users reported problems. The Online Tutorial link in is added in Help. This will provide a future link for the ongoing new Help development. In Amperometirc analysis, the manual detection now includes ability to select the end of peak. This helps for precise calculation of the area under curve. Furthermore, the program now reports event duration in the results spreadsheet. For detection parameter settings in the main window the freezing problem is fixed. The awkward input text box is replaced by convenient input box for each detection parameter. Users can now add and view File Comments for the event file. The command is located under File menu of the main window. 7. 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. 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