README to CellASIC-Pulse-Width-Modulation
A set of m-files (referred to hereafter as RxPWM) are created to deliver arbitrary concentrations of drug at arbitrary times to cells using the ONIX microfluidic system by CellASIC. In essence, pulse-width-modulation (PWM) is used to deliver any concentration of drug between 0 and the concentration of drug found in a sourcing well.

As of 11/6/2011 PWM has not been shown to be viable in delivering arbitrary drug concentrations. In other words, caveat emptor.

RxPWM runs in the MATLAB environment. RxPWM will accept a pair of vectors that contain a normalized 'drug signal' and a vector of the same length representing time. The units of time are assumed to be minutes. RxPWM will interpolate the drug signal using splines or lines and create a PWM signal at the resolution of the carrier frequency. The carrier frequency can be specified by the user. However, it has a lower limit set by the physical limitations of the pumps in the ONIX system.

The lower limit is defined as follows: The minimum switching time of the ONIX pump valves is defined as the smallest permissible duty cycle chosen to be 5%. Based on the ONIX spec sheet of the valves, they have a 5 ms or less "ON" and 4 ms or less "OFF". Since it is unclear how much drug will actually be delivered during a rapid "ON"/"OFF" pulse of 9ms, an estimation of the drug delivered is made. Assuming drug concentration linearly rises from 0 to MAX (or MAX to 0) during the "ON" (or "OFF") interval, a rapid "ON"/"OFF" is approximately a 4.5 ms pulse of MAX drug concentration. The error in the estimation can be reduced by increasing the time spent "ON". If the minimum pulse width is chosen to be 18ms, then the worst case scenario is a 20% error of drug delivered at 5% duty cycle, an acceptable error in most situations. The minimum carrier frequency is therefore decided to be 20*18ms = 360ms = 2.78Hz @ 50% duty cycle. The carrier frequency should be much higher than the frequency content in the modulated waveform.

The 5% cutoff limits pulses to duty cycles between 5% and 95%. Note that a calculated duty cycle of less than 5% is rounded to 0%, and a calculated duty-cycle of more than 95% is rounded to 100%.

The output of RxPWM is either an m-file that contains code sufficient for interfacing with the ONIX machine through microManager or a text file that can be imported into the ONIX software provided by CellASIC.

By default, the modulated waveform is converted into PWM using the sawtooth method. By default, the pulses always begin "ON". Options to change these defaults are forthcoming and include symmetric pulses.

There is also an option to set the pressure the ONIX valves apply to each well, which leads to different flow rates. The default pressure is 2 PSI. It is interesting to ponder whether or not cells "see" the same concentration of a drug at different flow rates.

Author(s): Kyle Karhohs