stimgrid

Your stimulator cannot produce every pulse you write down. It sets current in fixed steps and timing on a fixed clock, so every value gets rounded. For an asymmetric pulse (for example a short strong first phase and a long weak recharge phase) that rounding quietly breaks the charge balance you designed. A rate of 130 Hz may also become 129.87 Hz.

stimgrid shows what your device will actually deliver, and finds the nearest pulse on the device's grid whose two phases carry exactly equal charge. Pure Python, no dependencies.

For electrical neurostimulation and microstimulation on multi-electrode arrays (MEAs), microelectrodes and neural interfaces, with presets for the Intan RHS2116, Multi Channel Systems STG4000 and STG5, Tucker-Davis Technologies IZ2 and Cortical Labs CL, and support for any other current-controlled stimulator from its current and timing steps.

Research use only. stimgrid works from the resolution you give it (or a preset's published figures). Check the result on your own hardware and settings.

Install

Requires Python 3.9 or newer, and nothing else.

pip install git+https://github.com/sanjeevmuthusamy/stimgrid

Or from a downloaded copy, inside the stimgrid folder:

pip install .

This gives you the stimgrid command. You can also run it without installing, from the folder, as PYTHONPATH=src python -m stimgrid ....

Quick start

1. Find your device. stimgrid devices lists the built-in presets and where their figures come from. If yours is not there, give its own steps instead (see Devices).

2. Check your pulse. Give the first phase, the second phase and the rate:

   stimgrid quick --device mcs-stg4000 --amplitude-ua 7.3 --width-us 117 \
     --second-amplitude-ua 1.9 --second-width-us 450 --frequency-hz 130
   

3. Read the result (see Reading the output). Use the balanced pulse, or one of the options, in your stimulation software.

4. Save it for later or for a lab mate as a request file, and rerun it with stimgrid fit my_pulse.json.

Leave out --second-amplitude-ua and --second-width-us for a symmetric pulse; the second phase then copies the first.

Reading the output

For the quick start command above:

device: mcs-stg4000 (1.6 mA version): 20 µs time steps, 0.2 µA steps, max 1600 µA
  plan      7.3 µA x 117 µs | gap 0 µs | 1.9 µA x 450 µs
  rounded   7.4 µA x 120 µs | gap 0 µs | 2 µA x 460 µs
            charge 0.888 nC (+3.97% vs plan), net -0.032 nC, imbalance 3.4783%
  balanced  7.2 µA x 120 µs | gap 0 µs | 1.8 µA x 480 µs
            charge 0.864 nC (+1.16% vs plan), net 0 nC, imbalance 0.0000%
  option 1  7 µA x 120 µs | gap 0 µs | 2 µA x 420 µs
            charge 0.84 nC (-1.65% vs plan), net 0 nC, imbalance 0.0000%
  ...
  rate      frequency_hz 130 Hz -> 129.87 Hz (385 steps per period, -0.100%)

WARNING SG201 simple rounding leaves the pulse unbalanced (imbalance 3.4783%, net -0.032 nC per pulse)

best pulse: {"amplitude_ua": 7.2, "width_us": 120, "second_amplitude_ua": 1.8, "second_width_us": 480}
result: OK

Here the planned pulse would leave 0.032 nC on the electrode with every pulse; the balanced one leaves none and keeps charge per phase within 1.2% of the plan.

Another example: Intan RHS2116

An asymmetric pulse on an Intan RHS2116 with 0.1 µA steps, driven at 30,000 samples/s:

stimgrid quick --device intan-rhs2116 --step-ua 0.1 --sample-rate-hz 30000 \
  --amplitude-ua 7.3 --width-us 117 --second-amplitude-ua 1.9 --second-width-us 450 --frequency-hz 40

device: intan-rhs2116 (step 0.1 µA, 30000 samples/s): 33.3333 µs time steps, 0.1 µA steps, max 25.5 µA
  plan      7.3 µA x 117 µs | gap 0 µs | 1.9 µA x 450 µs
  rounded   7.3 µA x 133.333 µs | gap 0 µs | 1.9 µA x 466.667 µs
            charge 0.97333 nC (+13.96% vs plan), net 0.08667 nC, imbalance 8.9041%
  balanced  7.2 µA x 100 µs | gap 0 µs | 1.8 µA x 400 µs
            charge 0.72 nC (-15.70% vs plan), net 0 nC, imbalance 0.0000%
  option 1  7.2 µA x 133.333 µs | gap 0 µs | 1.8 µA x 533.333 µs
            charge 0.96 nC (+12.40% vs plan), net 0 nC, imbalance 0.0000%
  ...
WARNING SG201 simple rounding leaves the pulse unbalanced (imbalance 8.9041%, net 0.08667 nC per pulse)
WARNING SG203 the balanced pulse changes charge per phase by -15.7%

Simple rounding would leave 0.087 nC behind on every pulse. stimgrid lists exactly balanced pulses instead, closest to your plan first, and warns when the grid forces charge per phase to move.

How it works

1. Rounded. Each amplitude, phase width and gap is rounded (halves up) to the device's steps and clamped to its ranges. This is what you get if you type the plan in and let the device round it.
2. Balanced. stimgrid searches small changes to both phases, mostly the second phase's width and amplitude, the usual balancing knobs. On a gridded device, balance is checked exactly, as whole current steps times whole time steps, so "balanced" means equal to the last bit. On a device with continuous amplitude it also tries the first-phase amplitude that keeps your planned charge exactly.
3. Ranking. Exactly balanced candidates are ranked by closeness to your plan, with first-phase charge counted double because it sets the effect. The best and three alternatives are shown.
4. Rates. Each rate is rounded to a whole number of time steps per period, and the delivered rate is reported.

Command options

stimgrid quick takes the pulse as flags. Amplitudes are in µA, times in µs, rates in Hz.

Both quick and fit also take:

stimgrid --help and stimgrid quick --help list them too.

Devices

All presets are current mode. The MCS range is the model version you bought (STG4000) or the range you select (STG5). The STG4000 160 µA version is left out because its official datasheet could not be confirmed.

Not included yet, because the vendor does not publish a current step or a timing step:

If you have one of these, describe it with your own numbers (below), or send the values from your manual and they can become a preset.

stimgrid devices prints each preset's source. The RHS2116 has no pulse timers; the host sets every edge, so its timing grid depends on your host software. Any other stimulator can be described by its own numbers:

stimgrid quick --time-step-us 10 --amplitude-step-ua 0.5 --max-amplitude-ua 100 \
  --amplitude-ua 20 --width-us 105 --second-amplitude-ua 4 --second-width-us 520

Fields: time_step_us (required), amplitude_step_ua (leave out for continuous), max_amplitude_ua, min_phase_us, max_phase_us, max_charge_per_phase_nc, max_frequency_hz.

Request files

{
  "stimgrid": 1,
  "device": {"preset": "intan-rhs2116", "step_ua": 0.1, "sample_rate_hz": 30000},
  "pulse": {"amplitude_ua": 7.3, "width_us": 117, "second_amplitude_ua": 1.9, "second_width_us": 450},
  "rates": {"frequency_hz": 40},
  "max_imbalance": 0,
  "keep_first": false
}

stimgrid fit examples/intan_asymmetric.json
stimgrid fit examples/intan_asymmetric.json --format json
cat request.json | stimgrid fit - --format pulse

A preset takes its options (step_ua, sample_rate_hz or range_ua, as in the table) and any device field to override, for example {"preset": "intan-rhs2116", "step_ua": 0.1, "max_amplitude_ua": 10} or {"preset": "mcs-stg5", "range_ua": 160}. Invalid input names the exact place, for example pulse: width_us must be a positive number.

--format pulse prints only the best pulse, in the common shape (amplitude_ua, width_us, second_amplitude_ua, second_width_us, gap_us), ready to paste into a protocol file or another tool.

Findings

Exit codes

From Python

from stimgrid import Pulse, Rates, fit, intan_rhs2116

report = fit(Pulse(7.3, 117, second_amplitude_ua=1.9, second_width_us=450),
             intan_rhs2116(step_ua=0.1, sample_rate_hz=30000), Rates(frequency_hz=40))
print(report.balanced.as_pulse(), report.balanced.imbalance)

Limits of this tool

• It models one pulse shape: rectangular phases with an optional gap. It does not model DAC settling, electrode impedance, channel-to-channel mismatch or the RHS2116's trim settings.
• Rates are assumed to fall on the same time grid as phase widths.
• Continuous amplitude means the device's real amplitude resolution is unknown; the reported amplitude may need rounding again on the hardware.

Citing

If you use stimgrid in published work, please cite it. GitHub's "Cite this repository" button gives the reference from CITATION.cff:

Muthusamy S. stimgrid (version 0.2.0) [Computer software]. https://github.com/sanjeevmuthusamy/stimgrid

Tests

python -m unittest discover -s tests

Licence

MIT. See LICENSE.