Data
File formats
What each window reads and writes. Every intermediate result is a MATLAB .mat file that the next window loads.
Recordings
| Format | Window | What is needed |
|---|---|---|
| LabChart export (.mat) | Extract LDF | data (all channels concatenated), datastart, dataend; optional samplerate (1000 Hz assumed when missing), titles, unittext. Stimulus on channel 6, LDF on channel 8. |
| TDT tank / block folder | Extract Ephys | Streams Whis (stimulus) and xRAW (raw); read with the TDT MATLAB SDK (TDTbin2mat) |
| Intan RHD2000 (.rhd)[22] | Extract Ephys | File format 1.0–3.x, traditional single-file layout; amplifier channels at 0.195 µV per bit; digital and ADC inputs as stimulus candidates. The notch-filter setting in the header is shown but not applied. |
| Open Ephys binary[23] | Extract Ephys | Recording folder (or a folder above it) with structure.oebin and continuous.dat (GUI 0.5 or later); samples × bit_volts; ADC channels and TTL lines as stimulus candidates; AUX channels skipped |
| NWB 2.x (.nwb)[21] | Extract Ephys | An ElectricalSeries in /acquisition or /processing (the first one; data × conversion); stimulus TimeSeries and trial / interval tables aligned to the series start |
| EEGLAB .set, FieldTrip .mat, BrainVision .vhdr, plain .mat | EEG Analysis | See EEG files |
| Image stack (.mat or multi-frame TIFF) | ROI Analysis | See Image stacks |
LDF files
| File | Written by | Variables |
|---|---|---|
| Cropped LDF | Extract LDF | stim, LDF, t (s, 0 at the crop start), Fs (Hz) |
| LDF trials | LDF Processing; Batch (LDF) | segmentedLDF (trials × samples), segmentedTime (s, 0 = onset), Fs |
LFP and MUA files
| File | Written by | Variables |
|---|---|---|
| LFP | Extract Ephys (Save LFP…) | lfp_data (channels × samples), lfp_channels, lfp_fs, t_lfp, stim_data, stim_fs, t_stim |
| MUA | Extract Ephys (Save MUA…) | mua_data, mua_channels, mua_fs, t_mua, stim_data, stim_fs, t_stim, filterParams |
| ERP / CSD export | LFP Analysis | t, y (ERP averaged over channels), erp_avg, erp_std, erp_channels, n_epochs, onset_times, erp_params, csd when computed |
| Spike sorting | MUA Analysis | SpikeResults (spike times, cluster IDs, waveforms), SpikeSortParams, clusterQuality, info (including info.clusterEdits) |
EEG files
One file per participant, all with the same channels and trial times. The EEG Analysis window reads what each file says was already done to the data and lists it in its Overview tab; nothing in the file is run. More on the EEG window.
| Format | What is read |
|---|---|
| EEGLAB .set (numbers inside, or in a .fdt file next to it) | Trials or a continuous recording with events, channel names and positions, reference, and the EEGLAB history (filters, re-reference, ICA, rejected trials, interpolated channels) |
| FieldTrip .mat (raw or timelock data) | Trials with trialinfo, channel names, electrode positions (elec) and the cfg.previous history |
| BrainVision .vhdr + .vmrk + .eeg (Brain Products Recorder or Analyzer, exports from EEGLAB / MNE) | Continuous recordings with their markers (S 1, R 2, …) or segments exported from Analyzer (the condition of each segment is its marker at time 0); 16-bit, 32-bit integer or float data, multiplexed or vectorised; channel units and resolutions; positions; the amplifier filters used when recording |
| Plain .mat | The numbers (channels × samples, or with trials in any order) and a sampling rate; a form asks what each variable is. Values in volts are converted to µV |
| File | Written by | Variables |
|---|---|---|
| EEG measures (.csv) | EEG Analysis (Export results…) | Participant, Condition, Value_uV, Latency_s (peak only), Trials, PeakAtEdge |
| EEG results (.mat) | EEG Analysis (Export results…) | results: ERPs of every participant and the grand average, settings, measures, statistics |
Image stacks
In
.matwithstackorframes(H × W × N grayscale or H × W × 3 × N RGB; otherwise the first variable is used)- Optional in the .mat:
timeVecort(one time per frame),roiMask(logical H × W) orroiMasks(H × W × K, optionalroiNames), used as the first ROIs - Multi-frame TIFF: RGB frames are converted to grayscale (mean of the colour channels); time = frame index
Out
- .csv:
Timeplus one column per measure (Intensity, Movement, DFF; with several ROIs<measure>_<ROI name>), orDiameter_px(+Diameter_standard_px,Replacedwhen robust); for a kymograph, a matrix (first row = time) - .mat: struct
resultswith the series (one row per ROI),roiMasks/roiNames,roiMask(ROI 1),lineStart/lineEnd,motionCorrectionandshifts, and the preprocessing and diameter settings
Result files
| File | Written by | Content |
|---|---|---|
| Feature table (.csv / .mat) | Signal Characterization | One row per series: Trial_Channel, PeakLatency_s, OnsetDelay_s, FWHM_s, AUCpos, AUCneg, RiseTime_s, DecayTime_s, PeakAmp, Integral; the .mat has data and colNames |
| Group values and report | Signal Characterization (Groups & statistics) | Per-animal values (.csv) plus _report.txt, or the full result (.mat) |
| Figures | Signal Characterization | PDF, SVG, EPS; PNG or TIFF at 300 / 600 dpi |
| Batch summary | Batch Processing | <name>_summary.csv, <name>_summary.mat (table summary and struct batch), <name>_log.txt |
| Session | Every analysis window | <name>.nasession.mat: variable session (app, versions, OS, date, inputs with MD5, settings, results, notes) |
| Report | Every analysis window | <name>_report.pdf: one A4 page |
NWB export
Export NWB… in Extract Ephys writes the processed LFP in volts to /processing/ecephys/LFP, the stimulus to /stimulus/presentation, and electrodes with the source channel names. With matnwb installed it uses the official schema classes.
Without it, a built-in minimal writer follows the NWB 2.7 layout but is not validated at run time and does not embed the schema; check such files with nwbinspector or pynwb.validate in Python. Subject metadata is not written.
Walkthrough: the demo recording in each format
The demo tank's first 6 s of channels 3–6, written as Intan, Open Ephys and NWB files by core/demo/demoFormats.m, loaded in Extract Ephys.
Not supported
- Intan stimulation files (.rhs) and the "one file per signal type / per channel" layouts.
- The legacy Open Ephys format (.continuous files).
- NWB 1.x and 3-D ElectricalSeries.
- Recordings larger than memory: files are read in full.
These are listed as open items in the roadmap.