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chyuminchyumin
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Added kilosort-compiled for versions 1, 2 and 2_5
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‎kilosort_no_license/kilosort-compiled/Dockerfile‎

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FROM ks-matlab-base
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RUN chmod 755 /usr/bin/mlrtapp/ks_compiled
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ENV PATH="/usr/bin/mlrtapp:${PATH}"
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RUN apt-get update -y
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RUN apt-get install software-properties-common -y
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RUN add-apt-repository ppa:deadsnakes/ppa -y
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RUN apt-get install git python3.8 python3.8-dev -y
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 1
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 2
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
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RUN apt-get install python3-pip -y
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RUN update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
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RUN pip install -U pip
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‎kilosort_no_license/kilosort-compiled/build.sh‎

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#!/bin/bash
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docker build -t spikeinterface/kilosort-compiled-base:0.1.0 .
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‎kilosort_no_license/kilosort-compiled/ks_compiled.m‎

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function ks_master(fpath)
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try
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set(groot,'defaultFigureVisible', 'off');
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% Load channel map file
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load(fullfile(fpath, 'chanMap.mat'));
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% Load the configuration file, it builds the structure of options (ops)
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load(fullfile(fpath, 'ops.mat'));
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useGPU = ops.GPU;
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% load predefined principal components (visualization only (Phy): used for features)
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dd = load('PCspikes2.mat'); % you might want to recompute this from your own data
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ops.wPCA = dd.Wi(:,1:7); % PCs
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% This part runs the normal Kilosort processing on the simulated data
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[rez, DATA, uproj] = preprocessData(ops); % preprocess data and extract spikes for initialization
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rez = fitTemplates(rez, DATA, uproj); % fit templates iteratively
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rez = fullMPMU(rez, DATA);% extract final spike times (overlapping extraction)
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rez = merge_posthoc2(rez);
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fprintf('merge_posthoc2 error. Reporting pre-merge result\n');
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% save python results file for Phy
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rezToPhy(rez, fullfile(fpath));
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catch
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fprintf('----------------------------------------');
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fprintf(lasterr());
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quit(1);
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end
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quit(0);
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end
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‎kilosort_no_license/kilosort-compiled/push.sh‎

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#!/bin/bash
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docker push spikeinterface/kilosort-compiled-base:0.1.0
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‎kilosort_no_license/kilosort2-compiled/Dockerfile‎

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FROM ks2-matlab-base
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RUN chmod 755 /usr/bin/mlrtapp/ks2_compiled
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ENV PATH="/usr/bin/mlrtapp:${PATH}"
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RUN apt-get update -y
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RUN apt-get install software-properties-common -y
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RUN add-apt-repository ppa:deadsnakes/ppa -y
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RUN apt-get install git python3.8 python3.8-dev -y
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 1
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 2
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
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RUN apt-get install python3-pip -y
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RUN update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
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RUN pip install -U pip
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‎kilosort_no_license/kilosort2-compiled/build.sh‎

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#!/bin/bash
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docker build -t spikeinterface/kilosort2-compiled-base:0.1.0 .
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‎kilosort_no_license/kilosort2-compiled/ks2_compiled.m‎

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function ks2_compiled(fpath)
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try
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set(groot,'defaultFigureVisible', 'off');
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% Load channel map file
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load(fullfile(fpath, 'chanMap.mat'));
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% Load the configuration file, it builds the structure of options (ops)
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load(fullfile(fpath, 'ops.mat'));
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% preprocess data to create temp_wh.dat
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rez = preprocessDataSub(ops);
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% time-reordering as a function of drift
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rez = clusterSingleBatches(rez);
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% main tracking and template matching algorithm
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rez = learnAndSolve8b(rez);
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% final merges
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rez = find_merges(rez, 1);
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% final splits by SVD
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rez = splitAllClusters(rez, 1);
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% final splits by amplitudes
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rez = splitAllClusters(rez, 0);
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% decide on cutoff
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rez = set_cutoff(rez);
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fprintf('found %d good units \n', sum(rez.good>0))
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fprintf('Saving results to Phy \n')
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rezToPhy(rez, fullfile(fpath));
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catch
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fprintf('----------------------------------------');
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fprintf(lasterr());
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quit(1);
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end
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quit(0);
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end

‎kilosort_no_license/kilosort2-compiled/push.sh‎

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#!/bin/bash
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docker push spikeinterface/kilosort-compiled-base:0.1.0
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‎kilosort_no_license/kilosort2_5-compiled/Dockerfile‎

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FROM ks2_5-matlab-base
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RUN chmod 755 /usr/bin/mlrtapp/ks2_5_compiled
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ENV PATH="/usr/bin/mlrtapp:${PATH}"
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RUN apt-get update -y
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RUN apt-get install software-properties-common -y
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RUN add-apt-repository ppa:deadsnakes/ppa -y
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RUN apt-get install git python3.8 python3.8-dev -y
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 1
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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 2
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
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RUN apt-get install python3-pip -y
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RUN update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
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RUN pip install -U pip

‎kilosort_no_license/kilosort2_5-compiled/build.sh‎

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#!/bin/bash
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docker build -t spikeinterface/kilosort2_5-compiled-base:0.1.0 .
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