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-labs armband demo
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4998301/
Predicting the risk for lymphoma development in Sjogren syndrome
An easy tool for clinical use
Sofia Fragkioudaki, MD,a Clio P. Mavragani, MD,a,b,c,∗ and Haralampos M. Moutsopoulos, MD, FACP, FRCP, MACRb,c
------------------------------
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
------------------------------------------------------------
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
------------------------------
------------------------------
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
------------------------------
------------------------------
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
------------------------------OS: CentOS Linux 7
Memory: 251.7 GiB
Processor: Intel® Xeon(R) CPU E5-2643 v4 @ 3.40GHz × 24
Graphics: Quadro P4000/PCIe/SSE2
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.
https://www.dell.com/community/Inspiron/Suspend-resume-problems-on-Ubuntu-18-04/td-p/6072410
1. I already had the Nvidia drivers installed and was already using them
2. sudo systemctl disable nvidia-fallback.service
3. Edited /etc/default/grub and added the line :
GRUB_CMDLINE_LINUX=”nouveau.blacklist=1″
4. sudo update-grub
5. Restarted the laptop
wget http://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_418.87.00_linux.run
sudo sh cuda_10.1.243_418.87.00_linux.runQT is required for yakuake
sudo apt-get install build-essential
sudo apt-get install qtcreator
sudo apt-get install qt5-default
sudo apt-get install qt5-doc
sudo apt-get install qt5-doc-html qtbase5-doc-html
sudo apt-get install qtbase5-examples[installing yakuake (pull-down terimnal)]sudo apt-get install yakuake
install docker
run sudo service docker start
share docker daemon on windows and wsl
Export and import WSL environment:
wsl –export Ubuntu-18.04 ubuntu.tar
sudo apt update
sudo apt install snapd
sudo snap install code-insiders --classicadd alias code='code-insiders in .bashrc
Also Installed npm (permission), yarn, docker and Matlab 2019b
