[ANN] NeuroAnalyzer.jl

Specific Domains Biology, Health, and Medicine
21

NeuroAnalyzer.jl : Neurophysiological data analysis with Julia

v0.24.7 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl

  • stim: tdcs_dose(), tacs_dose(), tpcs_dose() – calculate effective parameters of tES dosages
  • process: filter_create() – new filter type: weighted least-squares FIR filter
  • gui: iview() can show bad channels
  • process: erp() – baseline segment is defined by two time points, may be subtracted before or after averaging
  • analyze: PSD- and spectrogram-, EROS-, EROP-related functions – log scaling of frequencies removed, moved to plotting functions
  • code cleanup
  • many minor additions and fixes
3 Likes
22

NeuroAnalyzer.jl : Neurophysiological data analysis with Julia

v0.24.8 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl

  • breaking change: channels are addressed by their labels, not numbers (breaking change); to convert numbers to labels, use get_channel(obj, type="eeg") or get_channel(obj, ch=["Fp1", "Fp2"])
  • breaking change: channels are stored as they are in the recording (physical order); list of channels sorted by their type is stored in OBJ.header.recording[:channel_order] (logical order)
  • breaking change: channels label is stored in OBJ.header.recording[:label], channel unit is stored in OBJ.header.recording[:unit]
  • list of bad channels is stored in the OBJ.header.recording[:bad_channel]
  • utils: get_channel()
    • channels may be addressed by name, e.g. ch="Fp1" or ch=["C3", "C4"] or by type, e.g. ch="all", ch="eeg" or ch=["mag", "grad"]
    • supports exclude options (default value is “bad”, so bad channels are excluded from the list)
  • initial support for MEG data
  • io: import_fiff() – both MEG and EEG data
  • gui: iview() – lots of changes:
    • select time segment
    • delete time segment / epoch
    • left click channel label to display its properties
    • right click channel label to mark it as bad
    • zoom in and out
    • scroll with mouse wheel
    • toggle scale bars, monochromatic mode, snapping
  • plot: plot_signal() – lots of changes:
    • finally displays properly data with > 100 channels
    • gets list of bad channels from the header
    • channels of different type are not displayed separately, but in logical order
    • scale bars and units are drawn for each channel type
  • process: denoise_cwt() – denoise using continuous wavelet transformation
  • process: remove_cwt() – remove artifacts using continuous wavelet transformation
  • analyze: cwtspectrogram() – improved CWT scaleogram
  • analyze: psd() – new methods: :gh, :cwt
  • code cleanup
  • many minor additions and fixes
2 Likes
23

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.24.9 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl

  • gui: iview():
    • butterfly / mean mode
    • time/epoch slider
  • gui: ipsd():
    • time/epoch slider
    • new channel selector
  • gui: ispectrogram():
    • time/epoch slider
    • new channel selector
  • gui: itopo():
    • time/epoch entry field
    • compatible with EEG/MEG
  • gui: iview_ica():
    • preview and remove ICA components
  • code cleanup
  • many minor additions and fixes
2 Likes
24

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.24.10 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl

  • return types added to all functions for better error handling
  • code cleanup
  • many minor additions and fixes
5 Likes
25

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.24.11 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl

  • plot: plot_heatmap()
  • tested against Julia 1.11 release
  • code cleanup
  • many minor additions and fixes
1 Like
26

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.24.12 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • io: import_ft() – FieldTrip EEG, MEG, events
  • io: import_fiff() imports SSP projections
  • gui: iedit() – move locs origin
  • process: generate_ssp_projectors() and apply_ssp_projectors()
  • code cleanup
  • many minor additions and fixes

Breaking changes:

  • markers field description renamed to value
  • MEG recording header must contain SSP labels, SSP channels and SSP data fields
1 Like
27

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.1 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • io: import_ft() imports EEG channels data for MEG+EEG recordings
  • analyze: lat_idx() – calculates lateralization index
  • analyze: tpt_detect() and tpt_analyze() – detects and analyzes pinches in TPT recordings
  • recorder: tpt() – records Two-point Pinch Test
  • channels list may now be defined using Julia regex, e.g. plot(eeg, ch=r"Fp.*")
  • new data types: TPT
  • code cleanup
  • many minor additions and fixes
2 Likes
28

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.2 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • gui: ifilter() – interactive filter design
  • code cleanup
  • many minor additions and fixes
2 Likes
29

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.3 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • Julia ≥1.11 is required
  • greedy threads scheduler is used: significant speed increase of many functions
  • statistical functions moved to (NeuroStats.jl)
  • code cleanup
  • many minor additions and fixes
2 Likes
30

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.4 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • breaking change: channel_cluster() returns channel numbers, not names
  • breaking change: referencing changes locs labels
  • plot: default palette changed to bluesreds for some plots (topomap, heatmap, matrix)
  • exclude_bads preference was added (default is false) to automatically ignore channels marked as bad from analysis
  • all tutorials are automatically generated using Quarto-based Markdown notebooks
  • code cleanup
  • many minor additions and fixes
31

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.5 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • plot: plot_connectivity_circle()
  • plot: plot_heatmap(), plot_topo() and plot_spectrogram() now can also draw thresholded region
  • analyze: topo_var(), diss(), gfp() and gfp_norm() for ERP/ERF objects
  • code cleanup
  • many minor additions and fixes
1 Like
32

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.6 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • code cleanup
  • many minor additions and fixes
33

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.7 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • analyze: entropy() – calculates sample entropy and normalized sample entropy
  • analyze: hfd() – calculates the Higuchi fractal dimension
  • analyze: sumsim() – calculates summed similarity using an exponential decay model
  • code cleanup
  • many minor additions and fixes
2 Likes
34

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.8 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • tester: iavh() – interactive module for subjective recreation of auditory hallucinations
  • analyze: dirinrg() – calculate Dirichlet energy
  • model: efield2d() – model 2-dimensional electric field
  • plot: plot_efield2d() – plot 2-dimensional electric field
  • NeuroStats.jl merged with NeuroAnalyzer.jl
  • Markdown documentation is no longer maintained
  • code cleanup
  • many minor modifications and fixes
3 Likes
35

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia

v0.25.9 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • breaking change: time points are internally rounded to 3 digits
  • updated tutorials
  • updated documentation format
  • plot: plot_phase() – plot phases
  • plot: plot_fi() – plot instantaneous frequencies
  • plot: plot_hs() – plot Hilbert spectrum
  • plot: plot_imf() – plot IMFs produced by EMD
  • plot: plot_gridlocs() – plot a simplified plot of 10-20 EEG channels on a grid
  • plot: plot_spectrogram() – plot Hilbert-Huang spectrogram
  • analyze: hmspectrum() – calculate Hilbert marginal spectrum
  • analyze: hhtspectrogram() – calculate Hilbert-Huang spectrogram
  • analyze: zipratio() – calculate zip ratio of the object data
  • analyze: emd() – perform Empirical Mode Decomposition (EMD)
  • analyze: transform(), ftransform() and htransform() replaced spectrum() – Fourier and Hilbert transforms
  • process: reference_slap() – perform spherical Laplacian referencing
  • new preference: colors – enable/disable colored output
  • code cleanup
  • many minor modifications and fixes
2 Likes
36

NeuroAnalyzer.jl: Neurophysiological data analysis with Julia
v0.25.10 is out: AdamWysokinski/NeuroAnalyzer.jl: Julia toolbox for analyzing neurophysiological data - Codeberg.org

  • breaking change: process: filter_create() – order is not translated into attenuation, transition band width is required for :firls, :remez and :iirnotch filters
  • breaking change: process: new structure of discrete wavelet decomposition coefficients
  • updated tutorials
  • analyze: ghexp() – calculate Generalised Hurst Exponents (GHEs)
  • process: many changes in discrete and continuous wavelet decomposition functions
  • process: denoise_dwd() – denoise using discrete wavelet decomposition
  • plot: plot_dwc() – plot discrete wavelet decomposition coefficients
  • plot: plot_filter_response() – plot group delay for FIR filters
  • plot: plot_polezero() – plot filter poles and zeros
  • plot: plot_locs() – plot brain or head mesh together with electrodes
  • code cleanup
  • many minor modifications and fixes
1 Like