Subthreshold reconstruction Laboratory
SubLab uses large scale spiking activity to reconstruct subthreshold activity for individual units. The input spike file is a binary file consisting of pairs of 'doubles': Spike identity (unit number) and spike time (seconds).
"Reconstruction of in-vivo subthreshold activity of single neurons from large-scale spiking recordings" https://www.biorxiv.org/content/10.1101/673046v1
To run SubLab
Install Matlab or Octave.
SubLab is available as a function and as a script:
The function is called SubLab_Function.m and reconstructs the subthreshold activity with 1 millisecond resolution of one user-defined unit (targetNeuron) given a matrix (first row unit identities and second row time spike times in seconds) with the spike identities and spike times (spikeData).
[reconstruction_full, spikes_full] = SubLab_Function(spikeData, targetNeuron, maxNumberOfEpochs)
The function can be tested using the Test_SubLab_Function.m script.
The script is called SubLab.m. The script will ask you to give the path to the Matlab or Octave binary. This path can be pasted into the SubLab_Start.m for variable "matlabOctavePath". To find the path to the executable: Right-click on the matlab/octave application icon.
Default settings
By default the program runs 5 epochs of training. For a real reconstruction one should use 10 or more epochs. This information is stored in the maxNumberOfEpochs.txt file in SubLab.m. The algorithm uses a validation data set to decide the optimal epoch.
By default the program runs two threads:
ReconstructionTraining_ProcessCount = 2; % 40 on a Threadripper 2990WX (32 Core, 64Gb)
ReconstructionComplete_ProcessCount = 2; % 10 on a Threadripper 2990WX (32 Core, 64Gb)
myRate_ProcessCount = 2; % 10 on a Threadripper 2990WX (32 Core, 64Gb)
Simulation_ProcessCount = 2; % 10 on a Threadripper 2990WX (32 Core, 64Gb)