## Imec Probe (IM) Tab

In brief: Detailed settings for each probe.

On the `Devices` tab you checked the `enable` boxes for the probes you want to run and then clicked `Detect`.

Use this tab to configure parameters for each probe, individually.

Topics:

- All Probes
  - Calibration Policy
  - Low Latency Mode
  - Vigilant Mode
  - Acquisition Start Signal
  - Survey all probe banks
    - Max bank
  - Filtered Streams
- Probe Database
- Table Viewing and Sizing
- Measured Sample Rate
- Editing
  - LED
  - IMRO Table
  - Bad (Stand-by) Channels
  - Channel Map
  - Save Channels
    - Force LF to Complement Listed AP Channels
    - Max Row Controls
- Fix Probe ID
- Default
- Copy

## All Probes

A few settings are common to all the probes…

### Calibration Policy

Select how the imec-provided ADC and gain calibration files for each probe are handled:

- Absolutely required.
- Used if you have that probe’s files, skipped otherwise.
- Skipped for all probes.

### Low Latency Mode

This mode runs the probe (and Obx ADC) sample fetching loop faster, which reduces the time to get fresh data. However, this drives the CPU 50%+ harder and reduces the maximum number of probes you can safely run concurrently. Pay attention to the Metrics Window and Task Manager Performance readouts to make sure your runs are stable under load.

### Vigilant Mode

If you are running probes, and if the `Vigilant` box is checked, the computer is commanded to stay awake during the run. This reduces system latency when responding to sudden surges in background activity. It can help an underperforming CPU avoid POP errors and keep up with high channel count acquisition. The downside is the computer runs warmer and the lifespan of thermal paste may be shortened. So we advise using Vigilant mode only if your system is not performing adequately. We found that might be the case when running quad-base probes on a laptop with a lower performance Core-Ultra CPU, for example, Mercury Lake.

### Acquisition Start Signal

Currently we are only supporting software-based initiation of imec data streaming. That is, the data acquisition starts manually when you click the `Run` button in the configuration dialog.

### Survey all probe banks

To do a run that is automatically customized for whole-probe surveys:

- Check the box in this item group.
- Select the number of seconds to allow probes to settle when run starts; (this is added to the recording time of the first bank).
- Select the number of seconds to record in each bank.

The entire surface of each selected probe will be sampled: shank-0:[bank-0..bank-max], shank-1:[bank-0..bank-max], etc.

> NXT probes use a block pattern covering them with fewest steps.

Although the survey controls the selected sites (looping over shanks and banks), it adopts the reference, gain, and highpass filter settings set in each probe’s current IMRO table. That is, you can thus choose to do the survey with external or tip referencing by setting that choice for each probe in the IMRO editor.

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

One (bin/meta) file-pair is saved for each probe. Within a file the sampling blocks are end-to-end. Open these files with the File Viewer (Ctrl-O) and open the Shank Viewer. As you scroll through the file the Shank Viewer shows the current probe region.

If enabled the sync waveform and/or the nidq stream are also recorded during a survey run. Using the linking feature of the File Viewer you can view probe activity with concurrent trigger events such as neural stimulations. These features enable you to program the most relevant regions of interest into the IMRO tables.

Note that the time to program a new bank plus amplifier settle time is about 2 to 3 seconds. You’ll definitely see these transition regions as you browse the data.

#### Max bank

In this mode all channels are saved, so the `Save chans` table column instead becomes `Max bank`. Use this item to skip sampling banks that are out of the brain.

### Filtered Streams

As of SpikeGLX version 20230425, you can set up a filtered probe AP-band stream that runs in parallel with the raw stream. You can set the bandpass edges for this stream, and the stream automatically gets global `demux` CAR. These data are required for SpikeViewer, and when present, are used to improve signal-to-background in both audio output and ShankViewers. There is a checkbox to disable this feature if you are running out of RAM or CPU, but we don’t think this will be necessary unless you are running as many as (12) 384-channel, or, (3) 1536-channel probes. It’s a good idea to look at the Metrics Window for any signs of instability.

> A filtered stream will auto-disable for a few seconds if the system is overstressed. When that happens, the filtered data are replaced by zeros, hence, ShankViews will appear black and audio will shut off.

## Probe Database

SpikeGLX maintains a database of probe settings in the _Calibration folder. The settings are keyed to the probe’s serial number. There is one entry per probe, hence, the software remembers the last thing you did with that probe. The entries are each time-stamped. Individual entries are discarded after three years of disuse.

When you click `Detect` we look for each selected probe in the database. If found, the stored settings are used. If no entry is found, the probe gets default settings.

You can always see and edit those settings using the `Each probe` table on the `IM Setup` tab.

Upon clicking `Verify` or `Run` the table values are transferred to the database for future runs.

## Table Viewing and Sizing

- The probe table scrolls!
- Resize columns by clicking on the dividers between column headers.
- Double-click on a divider to auto-size that column.
- Drag the `Configure` dialog’s outer edges or corners to resize all content.

## Measured Sample Rate

Not editable.

This is the probe’s (headstage’s) measured sample rate as determined by the calibration procedures on the `Sync` tab (See User Manual).

## Editing

- Select a table row, then click `Default`, or,
- Double-click in a table cell to edit that item.

For each probe, you can edit its:

- LED (really, for each headstage).
- IMRO table.
- Bad (stand-by) channels.
- Channel map.
- Save channels.

More details below.

### LED

One checkbox per probe, but really the LEDs are on headstages…

- NP 1.0-type probes: One probe per headstage: no conflicts.
- NP 2.0-type probes: Two probes per headstage: requires your thought.

When you click `Verify` or `Run` you will be warned if your LED settings for the same headstage conflict.

### IMRO Table

Use the graphical IMRO editor to select:

- Regions of interest (“boxes”).
- Which reference to use (external, tip).
- AP and LF gains and filters (where applicable).

### Bad (Stand-by) Channels

Edit directly in the table cell by specifying a channel list, just as you do for saved channels. E.g., 0:3,200,301:305.

The probe API lets you turn off the amplifiers for selected channels; what imec terms setting the channel to stand-by mode. The channel is still read out but its amplitude will effectively be zero. This makes graph windows easier to view. There is another more important way we use the bad channel list…

SpikeGLX and CatGT observe the geometry map that’s stored in every recording’s metadata file. A geometry (geom) map describes:

1. Where that channel’s electrode is on the probe.
2. Whether that channel should be `used` in spatial averaging (CAR).

When you click `Verify` or `Run`, SpikeGLX updates the probe’s geom map. These channels are set to (used=0):

- On-shank references.
- Listed bad channels.

### Channel Map

This lets you group/sort/order the channels in SpikeGLX graph windows. It has no effect on how binary data are stored.

### Save Channels

You can save all of the channels being acquired by setting the list to any of:

- blank
- ’*’
- ‘all’

You can save any arbitrary subset of channels using a printer-page-like list of individual channels and/or ranges, like: 1:200,205,207,350:360.

> The SY channel is always added to your list because it carries error flags and the sync channel.

#### Force LF to Complement Listed AP Channels

(If checked) AND (if this probe type has separate LF channels) THEN your list of saved channels is edited so that there is a saved LF channel for each listed AP channel. It’s just a convenience.

> The checkbox actually applies to all probes, not just the one being edited.

#### Max Row Controls

These edit the existing list to only keep AP channels that are between the tip of the probe and a specified maximum along the shank. The maximum can be given as a row number or as the distance from the tip.

## Fix Probe ID

This tool allows you to alter the stored serial number and part number of the selected probe. It is useful when a probe has a faulty EEPROM chip. The new values that you enter here will be used for this run. However, the values are not stored, so you will have to use the tool again for each run.

## Default

This is a handy way to set all of the editable fields:

- LED: off.
- IMRO: bank 0, external referencing, medium gain, AP filter on.
- Bad chans: read from the probe database.
- Channel map: ordered from probe tip to base.
- Save chans: all.

## Copy

Select a probe and copy its settings to a specified other probe, or to all other probes.

- This only acts between probes of the same `type`.
- This does NOT copy `measured sample rates`.
- This does NOT copy `bad chans`.

fin