## Sync Tab

In brief: Mapping Time Across Streams

## Square Wave Source

Choose `Disable sync waveform` to run without active alignment to edges of a common square wave. The software will still apply the measured sample rates for streams that have previously been calibrated.

Otherwise, a generator source should be programmed to form a simple square wave with a 1 second period and 50% duty cycle. You have three choices for the generator:

- `Separate high precision pulser` allows you to provide any waveform generator you like for the purpose.

- `Current NI acquisition device` will program your multifunction NI device to produce the required waveform at terminal `Ctr1Out (pin-40/PFI-13)`. (Brian Barbarits will make a simple breakout connector available to allow Whisper users to access this signal.) Digital devices like the 6535 are programmed to make the waveform on `line-0`.

- `Imec slot N` will program the indicated BS (PXI or OneBox) to produce the sync waveform and make it available at its SMA connector.

Whichever pulser source you select, the programmed (set) period is 1 second, but the actual period may differ from that. If you have measured the actual period of the generator's output with a high precision frequency/period analyzer, then enter that value in the `Measured period` box. If you have not measured it, enter 1 in the box.

> The calibration procedure measures the rates of clocks relative to the square wave generator clock. You should use the same generator for real runs that you use for the calibration.

## Imec, OneBox SMA Connectors

Each imec PXI BS card has a single SMA connector 'TRIG' on its front panel. Each OneBox has a Sync connector on its back panel 'SMA 1.'

In a PXI chassis you might have more than one imec BS module. However, the modules share the (input/output) sync signal on chassis backplane line <7>. Hence, in all conditions, you should connect the entire set of PXI modules to the rest of the world via one and only one SMA connector.

Example: If an Imec PXI BS is selected as the source, all Imec BS modules in the chassis will automatically get the signal via the chassis backplane. Connect only the designated source SMA to other devices.

Example: Whenever the selected source is NOT an imec PXI slot, then all imec PXI modules are set to input mode, and will share whatever signal you connect to the specified input `Imec PXI SMA slot`. Connect only the designated input SMA to other devices.

Whenever any imec BS (PXI or OneBox) is not being a source, e.g. `Disable sync waveform` is selected, it is placed in input mode. In this mode it can record one TTL signal of your choice as bit #6 of the SY word. Each OneBox can separately record up to one TTL signal (at its sync SMA). A chassis with one or more BS modules will, as a whole, record up to one TTL signal at the designated input SMA, which is propagated on the backplane to all PXI streams.

All sync SMA connectors are compatible with 0-5V TTL signals.

## Nidq Input

If using an NI device with sync, you will always have to connect a wire to one of its analog or digital input terminals. Yes, even if that device is selected as the sync source!!

At this time, Whisper boxes do not allow access to digital inputs, so you must connect the square wave to one of the multiplexed auxiliary analog inputs (MA).

## Calibration Run

To do a run that is automatically customized for sample rate calibration, check the box in this item group and select a run duration. We can't tell you how long is optimal. That depends upon how stable the clocks are and you can see that for yourself by repeating this measurement to see how it changes over time. It's probably a good idea to turn on power and let the devices approach a stable operating temperature before calibrating. We can't tell you how long that should be either. Our typical practice is 30 minutes of warm up and 40 minutes of measurement time. Note that a single calibration run can be done for as many devices at a time as you like.

A calibration run will save data files to the current run directory specified on the `Save tab`. The files will automatically be named `CalSRate_date&time_g0_t0...`

When the run finishes SpikeGLX will analyze the measured sample rates of all the selected devices and report the results in a dialog where you can adopt or reject them.

### Evaluating the Results

- Standard errors on measurements spanning 20 minutes or longer should be less than ~0.01 Hz. If larger, there is some instability to fix before trusting the measurement.

- If you are measuring a given clock for the first time, the difference from the manufacturer's uncalibrated rate should be less than ~2 Hz.

- If you are remeasuring a calibrated clock, the new and old rate should be within ~0.1 Hz of each other. Otherwise, one of the calibrations may have failed.

If you don't trust the results, do not click 'Apply.' Rather, try to find the problem, and then repeat the measurement. Good places to look for issues are the reported error and warning messages in the `Log` window. Also, try running with the `Metrics` window (Ctrl+M) open to look for warning signs. Note that imec error flags, which signify possibly dropped samples, are visible in the Metrics window and are always recorded in probe metadata files.

## Measured Samples/s

When you do a calibration run (and it is successful) the results are stored into your `_Calibration` folder. The next time you configure a run the results will automatically appear in the `meas` boxes on the {IM, OBX, NI} dialog tab appropriate to that stream.

Tabulated device calibration values are stored in the files:

- `_Calibration\calibrated_sample_rates_imec.ini`
- `_Calibration\calibrated_sample_rates_nidq.ini`

You can manually edit these if needed, say, if you've swapped equipment and already know correct rates from previous measurements.

fin