EMG forearm data

code classifier: http://www.sce.carleton.ca/faculty/chan/index.php?page=matlab

churchland lab antonio H Lara: raw data on dryad elife

BioPatRec dataset on EMG):

EMG with MRI validation: https://www.mdpi.com/1424-8220/20/3/724/htm

ctrl-labs

EMG dataset library on ResearchGate

Thomas Reardon 2018 CTRL-kit
https://www.youtube.com/watch?v=D8pB8sNBGlE&feature=emb_logo

Ctrl-kit by Nicholas Baker

Ctrl-labs armband demo

cosyne 2020 hifhlights

matt dormanski optotagged neuropixels data. long tracking data from moser lab richard gardner.

peter peterson collaboration on integrating behavior and neural recordings and have him as consultant.

future direction at the flatiron talk with mitya and eero simoncelli. control labs thomas and patrick. follow up with peter and

long term probe recording technic with Carl schooner. grip cement look up the probe fixation method with direct cementing using stoelting dental acrylic.

Peter Ledochowski and CSD based clustering of weak spikes.

Ottawa catherine toth starting april. voltage recording super cool.

irc2 v5.5.4 speed benchmark

single-thread, no-gpu

------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
    Recording file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
    Probe file:             ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
    Recording Duration:     1200.0s
    Data Type:              int16
    #Channels in file:      64
    #Sites:                 64
    #Shanks:                1
Pre-processing
    Filter type:            bandpass
    Filter range (Hz):      [300.0, 8000.0]
    Common ref:             trimmean
    Whiten:                 0
    FFT threshold:          8
    blank threshold:        0
Events
    #Spikes:                510735
    Feature extracted:      gpca
    #Sites/event:           18
    maxDist_site_um:        50
    maxDist_site_spk_um:    100
    spkLim_ms:              [-0.250, 0.750]
    #Features/event:        45
    #PC/chan:               2.500000e+00
Cluster
    #Clusters:              88
    #Unique events:         508992
    min. spk/clu:           30
    Cluster method:         drift-knn
    knn:                    30
    step_sec_drift:         20.0s
    batch_sec_drift:        300.0s
Auto-merge
    delta_cut:              1.000
    maxWavCor:              0.990
Runtime (s)
    Detect + feature (s):   156.2s
    Cluster runtime (s):    36.5s
    merge runtime (s):      12.4s
    Total runtime (s):      205.0s
    Runtime speed:          x5.9 realtime
    Processing speed:       2491.4 spikes/s
memory usage (GiB):         -0.018
    detect:                 -0.048
    sort:                   -0.018
    auto-merge:             -0.018
Execution
    irc2 version:           v5.5.4
    fGpu (GPU use):         0
    fParfor (parfor use):   0
    fLargeRecording:        0
    Parameter file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------

single-thread, gpu

------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
    Recording file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
    Probe file:             ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
    Recording Duration:     1200.0s
    Data Type:              int16
    #Channels in file:      64
    #Sites:                 64
    #Shanks:                1
Pre-processing
    Filter type:            bandpass
    Filter range (Hz):      [300.0, 8000.0]
    Common ref:             trimmean
    Whiten:                 0
    FFT threshold:          8
    blank threshold:        0
Events
    #Spikes:                510737
    Feature extracted:      gpca
    #Sites/event:           18
    maxDist_site_um:        50
    maxDist_site_spk_um:    100
    spkLim_ms:              [-0.250, 0.750]
    #Features/event:        45
    #PC/chan:               2.500000e+00
Cluster
    #Clusters:              84
    #Unique events:         502857
    min. spk/clu:           30
    Cluster method:         drift-knn
    knn:                    30
    step_sec_drift:         20.0s
    batch_sec_drift:        300.0s
Auto-merge
    delta_cut:              1.000
    maxWavCor:              0.990
Runtime (s)
    Detect + feature (s):   92.5s
    Cluster runtime (s):    20.3s
    merge runtime (s):      12.7s
    Total runtime (s):      125.4s
    Runtime speed:          x9.6 realtime
    Processing speed:       4072.3 spikes/s
memory usage (GiB):         0.049
    detect:                 0.049
    sort:                   0.049
    auto-merge:             0.049
Execution
    irc2 version:           v5.5.4
    fGpu (GPU use):         1
    fParfor (parfor use):   0
    fLargeRecording:        0
    Parameter file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------

12-thread, no-GPU

------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
    Recording file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
    Probe file:             ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
    Recording Duration:     1200.0s
    Data Type:              int16
    #Channels in file:      64
    #Sites:                 64
    #Shanks:                1
Pre-processing
    Filter type:            bandpass
    Filter range (Hz):      [300.0, 8000.0]
    Common ref:             trimmean
    Whiten:                 0
    FFT threshold:          8
    blank threshold:        0
Events
    #Spikes:                510735
    Feature extracted:      gpca
    #Sites/event:           18
    maxDist_site_um:        50
    maxDist_site_spk_um:    100
    spkLim_ms:              [-0.250, 0.750]
    #Features/event:        45
    #PC/chan:               2.500000e+00
Cluster
    #Clusters:              88
    #Unique events:         508992
    min. spk/clu:           30
    Cluster method:         drift-knn
    knn:                    30
    step_sec_drift:         20.0s
    batch_sec_drift:        300.0s
Auto-merge
    delta_cut:              1.000
    maxWavCor:              0.990
Runtime (s)
    Detect + feature (s):   58.3s
    Cluster runtime (s):    24.8s
    merge runtime (s):      9.4s
    Total runtime (s):      92.5s
    Runtime speed:          x13.0 realtime
    Processing speed:       5522.3 spikes/s
memory usage (GiB):         0.065
    detect:                 0.065
    sort:                   0.018
    auto-merge:             0.018
Execution
    irc2 version:           v5.5.4
    fGpu (GPU use):         0
    fParfor (parfor use):   1
    fLargeRecording:        0
    Parameter file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------

12-thread, GPU

------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
    Recording file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
    Probe file:             ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
    Recording Duration:     1200.0s
    Data Type:              int16
    #Channels in file:      64
    #Sites:                 64
    #Shanks:                1
Pre-processing
    Filter type:            bandpass
    Filter range (Hz):      [300.0, 8000.0]
    Common ref:             trimmean
    Whiten:                 0
    FFT threshold:          8
    blank threshold:        0
Events
    #Spikes:                510737
    Feature extracted:      gpca
    #Sites/event:           18
    maxDist_site_um:        50
    maxDist_site_spk_um:    100
    spkLim_ms:              [-0.250, 0.750]
    #Features/event:        45
    #PC/chan:               2.500000e+00
Cluster
    #Clusters:              84
    #Unique events:         502857
    min. spk/clu:           30
    Cluster method:         drift-knn
    knn:                    30
    step_sec_drift:         20.0s
    batch_sec_drift:        300.0s
Auto-merge
    delta_cut:              1.000
    maxWavCor:              0.990
Runtime (s)
    Detect + feature (s):   38.1s
    Cluster runtime (s):    15.2s
    merge runtime (s):      9.3s
    Total runtime (s):      62.6s
    Runtime speed:          x19.2 realtime
    Processing speed:       8152.4 spikes/s
memory usage (GiB):         0.018
    detect:                 0.018
    sort:                   -0.029
    auto-merge:             -0.029
Execution
    irc2 version:           v5.5.4
    fGpu (GPU use):         1
    fParfor (parfor use):   1
    fLargeRecording:        0
    Parameter file:         ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------

Computing resource

OS: CentOS Linux 7
Memory: 251.7 GiB
Processor: Intel® Xeon(R) CPU E5-2643 v4 @ 3.40GHz × 24 
Graphics: Quadro P4000/PCIe/SSE2

Aaditya Rangan’s missing value filling method

after filling the missing values with the median value per dimension do a low-rank approximation (svd) and re-project the matrix and repeat until the missing value vector values converge. It was tested to about ~70% missing matrix.

also, he runs a fast-tsne (Mannas’ implementation) followed by K-means to cluster the genetic data. Better discrimination when you apply missing-value filling procedure using the low-rank matrix method.