Radiens Manual

Radiens#

Radiens is two applications over one set of modules. Allego works against a live rig — it configures the hardware, streams the signals and records them. Videre works against a saved recording. Most modules appear in both, and where they do they are the same module: the same controls, reading live data in one app and a file in the other.

That is the idea to hold onto, because it is what makes the rest of this manual short. Learn Signal Metrics once and you know it in both places. The differences are at the ends — only Allego talks to hardware, so System and Impedance are its alone; only Videre opens files, so Data Sources, Curate, Neurons and Spectral are its alone.

Processing is layered and non-destructive in both apps. Filters in Signal Processing change what you see, never the file. A spike sort writes a separate, linked SPIKES set, and the sorted-unit modules read from it. The raw recording is never edited.

The modules#

Ordered as they appear in the Module Drawer — Curate pinned at the top, then Configuration, then Analysis.

Two sections follow that describe each application's window — Videre and Allego — and then one section per module, in the order above. Glossary and Shortcuts close the manual.

Videre#

Videre is the analysis app in Radiens: you work from a saved recording rather than a live rig. It opens XDAT, CSV, NEX5, Kilosort, and NWB files, and runs on Windows and macOS.

One idea organizes the whole app — a workbench of modules over a single open recording. Each module is a tab: Monitor for the signals, Signal Metrics for channel quality, Spike Sorter for sorting, 3D Model for anatomy, and so on. You open the tabs you need and arrange them into a dashboard. Every module reads the same recording and shares the same probe geometry, so a given channel or site is the same one in every tab.

Processing is layered and non-destructive. Filters in Signal Processing change only what you see, never the file. A spike sort writes a separate, linked SPIKES set — the raw data is untouched — and the sorted-unit tabs (Spike Grid, Raster, Neurons, 3D Model) read from it. Hold that model in mind and the rest of Videre follows.

What follows maps the Videre window. The modules themselves are covered one per section, in the order of the table above.

The Videre window#

Module Drawer. The Module Drawer runs down the left side of the window and lists every module as an icon. Open it with the arrow button in the top-left corner. Click a module to open it in a new tab, or to bring an already-open tab into focus. You can keep several tabs of the same module, and open any module in a new window to spread your work across monitors.

Dashboard. Arrange tabs to match how you work. Drag a tab header to move it, then drop it to split the view or stack tabs like a web browser. A live preview shows the layout as you drag.

Top Menu Bar. The top bar holds Settings and, on the right, your workspace controls and profile. Save Workspace stores the current tab layout. Restore returns your tabs to their saved positions the next time you launch Videre. The trash icon removes the selected tab from the saved workspace. Your profile, in the top-right corner, shows subscription status and the Videre version.

Playback Bar. The Stream Display bar sits along the bottom of the window and controls playback of the recording you are reviewing.

Open Datasets Menu. Drop-down menu of the open datasets (aka data files).

[!NOTE]

Like every Radiens app, Videre streams a recording from disk rather than loading it into memory, so a dataset's size is limited by your storage, not your RAM. The same design lets Videre run well across a wide range of machines — from a lab laptop to a dedicated workstation — on both Windows and macOS. And because Radiens is built on the principle that your data stays home, Videre works on your files where they already live: you point it at a recording rather than uploading it anywhere.

Allego#

Allego is the acquisition app in Radiens: you work against a live rig rather than a saved recording. It configures the acquisition hardware, streams the signals, and records them to disk.

The window follows the same idea as Videre — a workbench of modules over one session. Each module is a tab: System for the hardware, Monitor for the live signals, Signal Metrics for channel quality, Impedance for a site check. You open the tabs you need and arrange them into a dashboard. Every module reads the same stream and shares the same probe geometry, so a given channel or site is the same one in every tab.

Two modules are Allego's alone, because they act on hardware: System and Impedance. Both are absent from Videre's drawer.

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The Allego window#

Module Drawer. The Module Drawer runs down the left side of the window and lists every module as an icon. Open it with the arrow button in the top-left corner. Click a module to open it in a new tab, or to bring an already-open tab into focus. You can keep several tabs of the same module, and right-click a module to open it in a new window and spread your work across monitors.

Dashboard. Arrange tabs to match how you work. Drag a tab header to move it, then drop it to split the view or stack tabs like a web browser. A live preview shows the layout as you drag.

Top status bar. The top bar carries the Stream and Record buttons and shows how long the current stream and recording have been running. Settings opens from here.

Bottom status bar. The bottom bar reports the hardware you are actually connected to — the headstage on each port and the channel count. Check it before a session: it is the fastest confirmation that the rig in front of you is the rig Allego is configured for.

Workspace controls. In the upper right, Save Workspace stores the current tab layout, Restore returns your tabs to their saved positions the next time you launch Allego, and the trash icon removes the selected tab from the saved workspace. Your profile, in the top-right corner, shows subscription status and the Allego version.

Install and sign in#

Get the current build from the Radiens download page ↗ and take the file for your operating system.

Windows. Launch the installer. If Windows warns about an unrecognised app, choose More info, then Run anyway. Allego starts when the install finishes.

macOS. Open the installer and drag the Radiens app icon into Applications. Open Applications, then control-click the Radiens app icon the first time you launch it — that overrides the macOS security check, and is needed only once.

Linux. On a Debian-based distribution, download the .deb and install it with apt (for example, sudo apt install ./radiens.deb).

Sizing the machine is a separate question, and it is answered in Radiens System Requirements — the number that drives it is channel count times sample rate, not the app.

Your Radiens ID#

A Radiens ID is your account across Radiens apps, and it is your email address. Use the same ID everywhere so that your apps, licences and settings sit under one account.

To create one, launch Allego and wait for it to finish initializing. On the sign-up screen, choose Sign up now and fill in your details. Confirm the password on the next page and submit; a verification email arrives with a six-digit code. Enter the code, and you can sign in with that email and password.

[!NOTE]

The address you enter is your Radiens ID. Use one you will still be reading in three years — a lab address that survives a move is better than a personal one.

Hardware manuals#

Allego drives the instrument; the instrument has its own manual. For a SiNAPS system — the probe, the interface box, the cabling and power-up order, the self-calibration and the in-vivo protocol — see the SiNAPS Manual ↗ on neuronexus.com. Install Allego as described above first; the SiNAPS manual picks up from a running, signed-in Allego.

System#

System is where a live session is configured. In Allego you pick the acquisition hardware, set the sample rate, and choose which channels to record on each port — the settings that define what the rest of the instrument streams.

Where. Allego only, Configuration group — a toolbar for hardware and sample rate, a central table of signal sources and their channels, and cards for stimulus and GPIO features below.

It organizes the recording by signal source: the amplifier ports (Primary), the auxiliary analog inputs (AUX), the digital inputs and outputs (DIN, DOUT), and — on hardware that supports it — stimulation. For each source you select the channels to include and, on the amplifier ports, the cable delay used to keep them in sync. Additional cards expose stimulus, analog-out, digital-out, and trigger configuration. System is an Allego tab; its routing is locked while streaming or recording.

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System controls#

How to configure acquisition#

1. Open System in Allego and choose your Mode (the acquisition hardware).
2. Set the Sample Rate (some modes fix it).
3. In the Signals table, select the channels to record for each source — use Select All per row, or pick channels individually.
4. On the amplifier ports, set Cable Delay to Auto (or a fixed value) for synchronization.
5. If your hardware supports it, configure Stimulus, Analog Out, Digital Out, or Trigger in the cards below.
6. (Optional) Open Signal Map to verify the hardware-to-channel assignment. Routing locks once you stream or record.

See also — Impedance, check electrode connections after configuring hardware · Electrodes, probe and headstage geometry on each port · Signal Processing, the DSP pipeline that runs on this routing.

Electrodes#

Electrodes is where the recording learns its hardware. You tell it which probe and headstage sit on each port, and it builds the channel-to-site geometry that every other tab reads — so a channel in Monitor is the same site in Signal Metrics and the same point in 3D Model.

Where. Both apps, Configuration group — live against the rig in Allego, on an open recording in Videre. It shows the current port, its probe and headstage, and a view of the probe's sites.

The geometry defined here is shared, not per-tab. Set it once and the layout, site selection, and coloring follow through the whole app. You can span a large probe across ports, add more than one probe to a port when channels allow, and pull in GPIO channels (AUX, DIN, DOUT) alongside the amplifier signals.

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Electrodes controls#

How to set up a probe#

1. Select the Port you want to configure.
2. Click Edit to enter configuration mode.
3. Choose the Headstage and Probe for that port (leave them empty to disconnect).
4. If the probe needs more channels than one port provides, enable Multi-port probe.
5. Optionally add GPIO Channels to bring in TTL or other auxiliary signals.
6. Click Apply to save — the geometry is now shared across every tab.

See also — Data Sources, open the recording you are configuring · Signal Metrics, see per-site quality on this geometry · 3D Model, place these sites in a brain atlas.

Signal Processing#

Signal Processing is where you build the filter chain the rest of Videre sees. You add IIR filters and references, order them, and they apply to the signals as a pipeline — cleaning up line noise, isolating spikes or LFP, re-referencing across channels.

Where. Both apps, Configuration group — live against the rig in Allego, on an open recording in Videre. Three columns of filters — Hardware, Data and Visualization — with the controls to add and order them below.

The pipeline runs in stages, and the stage decides how permanent the effect is. Hardware and Data filters act on the recorded stream and are available for live acquisition; Visualization filters change only what you see and work on any open file. On a saved recording you work in the Visualization stage — the file is never rewritten. Each filter is channel- and sample-rate–aware.

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Signal Processing controls#

How to build a filter pipeline#

1. Choose a Stage — on a saved recording, use Visualization.
2. Choose an IIR Filters type (for example, Notch for line noise, then Bandpass for spikes).
3. Set the filter's parameters (frequencies, order, channels) in the panel that appears.
4. Click Add to place it in the stage.
5. Reorder with the up arrow so filters run in the order you want; edit or delete as needed.
6. Or start from a Preset (LFP, Single Unit, …) and adjust from there.

See also — Monitor, the Show monitor DSPs toggle applies this pipeline to the plot · HD Snapshot, compare filtered vs. raw with Apply Viz Filters · Electrodes, defines the channels the filters operate on.

Impedance#

Impedance is your pre-recording connection check. In Allego it measures each electrode site's impedance through the acquisition chip's built-in test circuit, and shows the result as a color-coded probe map plus a per-channel table — so a poorly connected or fouled site is obvious before you commit to a recording.

Where. Allego only, Signal Collection group — the probe map with a colour legend on the left and, after a run, a per-channel data table below.

You pick a port and whether to view magnitude (MΩ) or phase (°), then run the measurement. Warm sites read high impedance (a weak connection), cool sites read low — the map is the fast scan, the table is the exact number. Impedance is an Allego tab: it runs against live hardware and is disabled while streaming or recording so the test does not interfere.

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Impedance controls#

How to check impedance#

1. Open Impedance in Allego with the probe connected.
2. Select the Port to measure and set Field to Magnitude.
3. If the port has more than one probe, step Probe View to the one you want.
4. Click Run — the chip measures each channel and the probe map fills in.
5. Read the map: warm sites are high impedance (suspect); cool sites are good. Sort the table to list the out-of-spec channels.
6. Re-seat or clean the probe and Run again to confirm.

See also — System, hardware, ports, and sensor setup for acquisition · Signal Metrics, the complementary RMS-noise view of channel quality · SiNAPS Manual ↗ — a SiNAPS probe is checked by its self-calibration and heat map rather than here; this tab reads passive probes on the same rig..

Data Sources#

Data Sources is where a session starts. You point it at a folder of recordings, see what's there in a table, and open the file you want to work on — which loads it into the rest of Videre's tabs.

Where. Videre only, and the first tab in the Configuration group — a table of the recordings found in the selected folder, with the count and total size summarised at the bottom.

It reads the recording formats Videre supports and shows each file's key facts up front: type, date, duration, channel count, sample rate, and size. It also handles routine file housekeeping — copy, move, delete — so you can manage a dataset without leaving the app.

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Data Sources controls#

The table columns — name, type, date, duration, channels, sample rate, size — sort and filter, and the checkboxes select rows for opening or file operations.

How to open a recording#

1. Click Select Folder and choose the directory that holds your recordings.
2. Set Depth if the files are in subfolders (use all to search everything below).
3. Click Refresh to scan the folder.
4. Select one or more rows with the checkboxes.
5. Click Open File(s) to load them — the recording is now available in Monitor, Electrodes, and the other tabs.

See also — Electrodes, set the probe and headstage for the recording you opened · Monitor, view the signals from the file · Curate, build a processing pipeline over a dataset.

Monitor#

Monitor is where you watch the signals — streaming from the rig in Allego, or replayed from an open recording in Videre. Every selected channel is drawn as a trace, scrolling in time, with the controls to make the view readable: amplitude, time window, channel spacing, and a view-only bandpass filter.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. It opens on the multichannel plot: one row per channel across the current time window, view controls in the top bar, plot-scale controls along the bottom. A SiNAPS calibration is watched here, live (see the SiNAPS Manual ↗).

The plot is a view, not an edit. The bandpass filter and the DSP toggle change what you see, never the file — the same non-destructive rule that governs the rest of Videre. Playback is driven from the Stream Display bar at the bottom of the window (see Videre): scrub to any point in the recording and the traces follow.

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Monitor controls#

Top bar — view options for the plot:

Bottom bar — how the traces are scaled and drawn:

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How to review a recording#

1. Open Monitor from the Module Drawer (Analysis group).
2. Set the Amplitude Range and Time Window so the traces are readable at the scale you care about.
3. Optionally set a Low / High bandpass to clean up the view — for example, a high-pass to drop slow drift when you are looking for spikes.
4. Scrub with the Stream Display bar to move through the recording; the traces follow the playhead.
5. Switch Plot Type to Heatmap when you want a time-frequency view of the same channels.

See also — Signal Processing, the DSP pipeline the Show monitor DSPs toggle applies · Signal Metrics, per-channel quality once you have the view set · Electrodes, choose and color the channels you see here · HD Snapshot, draw every captured sample for a sample-accurate close-up.

HD Snapshot#

HD Snapshot is the close-up. Where Monitor resamples to keep playback smooth, HD Snapshot draws every recorded sample in a chosen window, stacked across all channels — so what you see is the waveform as recorded, with nothing decimated away.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. Channels stacked vertically across a single time window, with the navigation and window controls in the top bar.

You set a start time and a window duration, then step through the recording page by page. Because it renders full-resolution data, it works one window at a time rather than scrolling live; large arrays load on demand. Amplitude scale, channel height, and an optional visualization filter let you dial the view in for the detail you're after.

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HD Snapshot controls#

How to inspect a waveform#

1. Open HD Snapshot on a recording (open the file in Data Sources first).
2. Set Start Time to the moment you want and choose a Duration window.
3. Click Refresh (or View for a large array) to draw the snapshot.
4. Use Previous / Next page to step through the recording by the Step amount.
5. Open Settings to set Channel Height and a manual AMP Y Range for the detail you need.
6. Toggle Apply Viz Filters to compare the filtered and raw waveform.

See also — Monitor, the scrolling overview; HD Snapshot is the full-resolution zoom · Signal Processing, the filters Apply Viz Filters draws · Signal Metrics, find the channel worth a close look, then open it here.

Signal Metrics#

Signal Metrics answers "which channels are good?" at a glance. It computes a per-channel metric — RMS noise, spike count, a bad-channel flag — and paints it onto the probe as a color-coded heat map, so a noisy corner of the array is obvious before you commit to analysis.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. The probe heat map with a colour legend, and — when you turn it on — a per-site data table. This is the heat map a SiNAPS calibration is read from, running live in Allego (see the SiNAPS Manual ↗).

You pick the metric and the time window; the map colors each site accordingly, with a legend for the scale. Turn on the table for the exact numbers, sort to find the outliers, and set a custom color scale when you want to compare against a fixed threshold rather than the automatic range.

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Signal Metrics controls#

How to check channel quality#

1. Choose a Metric — RMS noise is the usual starting point.
2. Select the Port (and step Probe View if the port has more than one probe).
3. Set the Time Scope window if you want a longer look-back.
4. Read the heat map: warm sites are worse, cool sites are better; the legend gives the scale.
5. Turn on Table and sort to list the worst channels exactly.
6. Turn on Custom Scale and set Min / Max to judge sites against a fixed threshold.

See also — Electrodes, the probe geometry and channels this maps onto · Signal Processing, the filters applied before metrics are computed · Monitor, look at the traces of a channel the map flags.

Spike Grid#

Spike Grid lays the whole probe out as a grid of small waveform plots — one cell per channel — each showing the spikes detected on that channel over a recent window. It's the fast survey: scan the array, see where the units are, and judge whether your detection threshold is picking up real spikes or noise.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. A scrollable grid of per-channel spike waveforms.

Detection is driven by the spike thresholds, which you can open and tune from here. The grid pulls spikes from a lookback window you set, so you control how much history each cell summarizes. It's the entry point to the sorted-unit tabs — Raster, Neurons, and 3D Model read from the same detected spikes.

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Spike Grid controls#

How to survey spikes#

1. Open Spike Grid on a recording.
2. Set the Lookback window for how much history to summarize per channel.
3. Click Settings and adjust the detection threshold until real spikes are caught and noise is not.
4. Turn on Probe layout to read the grid in the probe's physical arrangement.
5. Use Zoom In / Out to fit the channel count you want to see at once.
6. Click Export graph to save the view.

See also — Spike Sorter, sort the detected spikes into units · Raster, the same spikes as event trains over time · Neurons, quality metrics for the sorted units.

Spike Sorter#

Spike Sorter turns detected spikes into neurons. It clusters the spikes into putative single units and writes the result as a separate, linked SPIKES set — your raw recording is never changed, and the sorted-unit tabs (Spike Grid, Raster, Neurons, 3D Model) all read from what it produces.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. The sort's summary statistics, quality gauges, and site- and unit-quality heat maps.

It's the hub of the sorting workflow, and it shows its work. A dashboard tracks the sort as it runs — SNR, noise, unit yield, and sort efficiency on gauges, plus per-site and per-unit quality maps — so you can judge whether the sort is healthy rather than waiting for a single final number. In Videre you sort an open file after the recording, or track a live sort as Allego writes it. When the sort finishes you can export the result to Phy.

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Spike Sorter controls#

(Live-acquisition controls — Sorter Active/Start, Rebase, Clear, Initialize, Update Period — appear when sorting live in Allego.)

How to sort a recording#

1. Open Spike Sorter on a recording.
2. (Optional) Click Settings to confirm the detection thresholds.
3. Click New Sort to start the sort.
4. Watch the dashboard — the SNR, noise, and yield gauges and the quality maps show how the sort is going; the Phase and Progress fields track it to completion.
5. When it finishes, click View Sort Details to inspect the clustering, or Export to Phy to hand the units to downstream tools.
6. Open Neurons or Raster to work with the sorted units.

See also — Spike Grid, set thresholds and see the spikes this sorts · Neurons, per-unit quality and spike-train analysis · Raster, the sorted units as spike trains over time.

Raster#

Raster reduces spikes to their timing. Each spike is a tick, each row is a channel or a sorted unit, and time runs left to right — so bursts, silences, and rhythms across the population show up at a glance, without the clutter of waveforms.

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. A raster of spike times — units when a sort is selected, channels otherwise — with a time-window slider along the bottom.

If a spike sort is active, the rows are the sorted units; otherwise they are raw channels. You choose the time span with a slider and can hide unsorted spikes to focus on real units.

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Raster controls#

How to read a raster#

1. Open Raster on a recording with a spike sort (see Spike Sorter).
2. Turn on Sorted Only to leave just the sorted units.
3. Drag the Time Window slider to zoom the time axis in or out.
4. Read the pattern — dense columns are synchronized firing; gaps are silence.
5. Click Export graph to save the view.

See also — Spike Sorter, defines the units shown here · Neurons, per-unit quality and spike-train statistics · Spike Grid, the waveform detail behind these ticks.

Neurons#

Neurons is where the sorted units become results. Once a spike sort exists, this tab shows each unit as its own plot in a grid — so you can judge unit quality and read out firing behavior across the whole population at once.

Where. Videre only, Analysis group — a paginated grid of per-unit plots, colour-coded by firing rate or quality label.

It has two modes. Spike Trains characterizes each unit on its own terms — inter-spike-interval histograms, average waveforms, and related analytics, sorted by a metric you choose. PSTH aligns firing to an event and shows the post-stimulus time histogram per unit. Because it reads from a completed sort, populate it from the Spike Sorter first.

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Neurons controls#

How to review sorted units#

1. Open Neurons on a recording that has a spike sort.
2. Stay in Spike Trains and pick an Analytic (for example, ISI histogram).
3. Set Sort By to bring the strongest units (e.g., highest SNR) to the front.
4. Set the Time Range — a lookback window, or a custom span you enter and plot.
5. Open Bin settings to tune the histograms; use Zoom In / Out and pagination to move through units.
6. Switch to PSTH, choose the event and trigger, and read each unit's response; Export to save.

See also — Spike Sorter, produces the units shown here · Raster, the same units as spike-time rasters · 3D Model, place these units in anatomical space.

3D Model#

3D Model puts your recording in anatomical space. It renders the probe inside a 3D brain atlas, places each recording site where it physically sits, and — when a sort exists — draws the sorted units as spheres colored by firing rate. It turns "channel 47" into "this spot in this structure."

Where. Both apps, Analysis group — live against the rig in Allego, on an open recording in Videre. A 3-D scene — brain volume, atlas slice and probe — with position, angle and display controls in a side panel.

You set the probe's position and angle relative to bregma or the surface, and the scene updates live. It supports rat, macaque, and organoid models, multiple probes on a port, and optional color-coding of sites by a signal-quality metric. The unit data comes from the Spike Sorter; the geometry comes from Electrodes.

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3D Model controls#

How to place a probe#

1. Open 3D Model and select the Port and Species.
2. Enter the Probe Position (X, Z, Y) and Probe Angle for how the probe was inserted; the scene updates as you type.
3. Drag in the canvas to orbit the view; use Zoom In / Out and Reset Camera to frame it.
4. Toggle Brain Volume, Atlas Slice, and Probe visibility to see through to the sites.
5. Turn on Site Signal Metrics and pick a metric to color the sites by quality.
6. With a sort loaded, read the unit spheres — size and color track firing rate.

See also — Electrodes, the probe geometry placed here · Spike Sorter / Neurons, the units shown in the scene.

Spectral#

Spectral moves from voltage to frequency. It computes power spectra and spectrograms over the channel groups and time ranges you define, so rhythms and band power — the LFP side of the recording — become the thing you read, not the raw trace.

Where. Videre only, Analysis group — a top toolbar of analysis parameters, a results panel, and a right-side panel of display settings.

The analysis is explicit: you choose the output (a spectrum or a time-resolved spectrogram), the method (periodogram, Welch, or STFT), the FFT window and overlap, and the frequency range. In Videre you work in Analysis mode — define trials, run the computation across every trial and group, then explore the results; Streaming mode renders live heat maps as data plays.

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Spectral controls#

How to run a spectral analysis#

1. Open Spectral and stay in Analysis mode.
2. Define your Channel Groups, and the Trials (time ranges) you want to compare.
3. Set the Output (Spectrum or Spectrogram) and the Method (Welch for averaged spectra, STFT for spectrograms).
4. Set the Windowing — window type, segment length, and overlap.
5. Click Run Analysis; watch the progress bar to completion.
6. Set the Freq Range and Units, then read the results — toggle trial and group visibility and adjust the layout to compare.

See also — Monitor, the time-domain view of the same channels · Signal Processing, the filters Signal Filters applies · Signal Metrics, per-channel noise before you analyze bands.

Curate#

Curate is a dataset-to-dataset pipeline builder. You lay out a flow graph — a source recording on the left, a chain of transform nodes in the middle, an output sink on the right — and it produces a new, processed dataset. It's how you standardize preparation: filter, re-reference, slice, downsample, remap, then run it.

Where. Videre only, pinned at the top of the Module Drawer — a flow canvas, with a palette of transform nodes on the left and the protocol and data-source details on the right.

The model is nodes and edges: each node is one transform, and data flows along the edges you draw between them. Save a pipeline as a protocol and apply it to the next dataset, so the same preparation is reproducible across a study. Curate is a workflow inside Videre — pinned to the top of the Module Drawer — not a separate application.

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Curate controls#

How to build a pipeline#

1. Select a Data file and drag a Source node onto the canvas; set its file and channels.
2. From the palette, drag the transform nodes you need — for example Bandpass Filter, then CAR Ref — and place them left to right.
3. Draw edges from each node's output port to the next node's input.
4. Right-click each node to set its parameters (cutoffs, reference channels, and so on).
5. Drag a Sink node to the end, connect it, and set the output file.
6. Click Save Protocol to store the pipeline, or Apply to run it — progress shows as it processes.

See also — Data Sources, the recordings that feed a pipeline · Signal Processing, the filter types used as transform nodes.

Glossary#

Definitions for the terms used across Radiens — from acquisition through analysis.

Hardware and channels#

• Probe — the silicon electrode array that records neural signals. Its geometry (site layout, shank count, spacing) threads through every Radiens view.
• Headstage — the amplifier that connects a probe to the acquisition system. Each occupied port has an assigned headstage type.
• Port — a physical input on the acquisition system to which a probe/headstage connects.
• Channel — the data stream from a single recording site. Addressed by a signal type and a native channel index, not by a single system-wide number.
• Signal type — the hardware bank a channel belongs to: PRI (amplifier), AUX (analog in), DIN (digital in), DOUT (digital out).
• Native channel index (ntvChanIdx) — the zero-based index of a channel within its signal-type bank.
• Signal group — a user-defined set of channels grouped for display and processing.
• Impedance — the electrical impedance of an electrode site, used as a quality-control metric for a viable recording connection.

Filters and signal processing#

• DSP — digital signal processing: the configurable stages applied to raw signals.
• Filter — a DSP stage (e.g. high-pass, low-pass, band-pass, notch) that shapes the signal; filters can be combined into DSP groups per signal type.
• RMS noise — the root-mean-square amplitude of a channel's noise floor.
• SNR — signal-to-noise ratio; a per-channel signal-quality metric.
• Threshold — the voltage level (absolute, or a multiple of the channel's standard deviation) above which a spike is detected.
• LFP — local field potential: the low-frequency component of the recorded signal.

Spikes, sorting and units#

• Spike — a detected action-potential event on a channel.
• Waveform — the voltage trace of a detected spike.
• Spike sorting — grouping detected spikes into clusters attributed to putative single neurons.
• Cluster / unit / neuron — a group of spikes assigned to one putative neuron.
• SPIKES set — the separate, linked dataset a spike sort writes. The sorted-unit tabs read from it; the raw recording is never changed.
• Raster — a plot of spike times (event trains) across channels or sorted units.
• Spectral / spectrogram — a time-frequency view: band power across channel groups over time.

Shortcuts#

Quick keys for moving through a recording and nudging the view.

Everything documented here is Videre. The transport keys step through a saved recording, which is a thing Allego does not do — it streams live. Allego's own shortcuts are not yet documented; they will be added here once confirmed against the application.

Playback transport (J / K / L)#

Videre uses the standard J / K / L media-transport convention for stepping through file playback:

Navigation#

Note: these are the transport and nudge shortcuts documented for the plot tabs. Tab-specific shortcuts (Spike Sorter, 3D Model, etc.) will be added here as they are confirmed.