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pulse counting

An electronic instrument will give output as square pulses whose amplitude will be maximum 3V. This output I want to connect to PCI card 6225 as analog signal for counting the number of pulses. Frequency of analog input will be maximum 5000 Hz. In one continous measurement, time will be of 5 minutes which can result into 1.5 million as number of pulses considering frequency as 5000Hz.  At one time, two channels will get the input and simultaneously my labview program should count both. Very high accuracy is required as this will be used to calibration system. Is this possible to handle by labVIEW? I am relatively new to this software and have LabVIEW 8.2 development version. Thanks in advance.
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If you're reading square pulses, why are you using an analog signal?  I'm pretty sure 3V will be enough to switch a digital input on the 6225 (you should confirm this with your hardware).  You can then use the two counter channels, which are capable of 80Mhz (plenty fast for your rate) and will count up to 2^32-1 (somewhere over 4 billion).  It's easy to set up and you'll get accurate readings.  Take a look at the Counter/Timer examples provided with LabVIEW.
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