Shield:

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Execute main analysis on all datasets

• anesthetized rat (arat)
• anesthetized mouse (amouse)
• opto-tagging experiments
• freely moving mouse (fmouse)
• model -> run EXECUTE_DATASETS() after write in VARIABLE_DEFINITIONS: funcCallDef = 'MAIN_ANALYSIS';

Attention:

1. You need to adjust all global varriable tables first:

• ANA_RAT_GLOBALTABLE
• ANA_MOUSE_GLOBALTABLE
• OPTO_GLOBALTABLE
• FREE_MOUSE_GLOBALTABLE
• MODEL_GLOBALTABLE

3. If you run optotagging project at first time you need to create a cellbase first!
4. If you want to simulate a model first:

• specify network parameters in MODEL_PARAMETER_DEFINITIONS
• specify global variables in MODEL_GLOBALTABLE
• run GENERATE_AND_SIMULATE_MODEL

5. If you want to simulate the model parameter- or vaiancespace:

• specify network parameter distributions in MODEL_PARAMETER_DEFINITIONS
• specify global variables in MODEL_GLOBALTABLE_PAR/MODEL_GLOBALTABLE_VAR
• run SIMULATE_PARAMETER_SPACE (for simulation)
• run EXPLORE_PARAMETER_SPACE (for processing results)

6. For model simulations make sure that you commented out the correct section in pacemaker_network_simulation.hoc (synaptic delays or decays are controlled)
7. In lot of codes ISSAVE argument of the functions is not logical, but flag variable (if specified -either true or false or whatever- it will save the rsults)

For the creation of publication figures, call MSSYNC_FIGURES with the appropriate target directory as a string argument

• cellbase (optotagging) - https://github.com/hangyabalazs/CellBase

• npy-matlab codes are added to basic CODEFOLDER (readNPY, etc.)

• hangya-matlab-code package - https://github.com/hangyabalazs/Hangya-Matlab-code

• install Neuron simulator: ...\MS_sync_codes\modelnrn-7.4.i686-pc-mingw32-setup.exe (modeling)

• clustering: Kilosort/ Kilosort2 (run on GPU: Matlab parallel toolbox and Visual Studio, actual versions on analysis computer: Matlab 2018a, Visual Studio 2013 (version12), Cuda 9.0): Matlab- Visual Studio compatiblity: https://www.mathworks.com/support/requirements/previous-releases.html Matlab -Cuda: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html Other compatible versions (with nvidia gtx 1080 GPU):

• Matlab 2016b+ Cuda7.5+visual studio 2013 or

• Matlab 2017b+ Cuda 8 + visual studio 2013 Download Kilosort: https://github.com/cortex-lab/KiloSort (Simply add to Matlab path the package) Download manual clustering package (python based): https://github.com/kwikteam/phy

• manual clustering Kilosort output: phy-GUI/ phy-GUI2

Please contact us with any questions, bug reports, and general feedback:

Barnabas Kocsis and Balazs Hangya
[email protected]
[email protected]