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Modeling realistic synaptic inputs of CA1 hippocampal pyramidal neurons and interneurons via Adaptive Generalized Leaky Integrate-and-Fire models (Marascoa et al., 2024)
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<html> <p>NEST patch and python files for the model: <a href=""> A. Marascoa, C. Tribuzi, C. A. Lupascu and M. Migliore. Modeling realistic synaptic inputs of CA1 hippocampal pyramidal neurons and interneurons via Adaptive Generalized Leaky Integrate-and-Fire models.</a> </p> <p>In this study we propose an Adaptive GLIF (A-GLIF) approach that can reproduce experimental findings under variable currents by incorporating a new set of update rules. The extended A-GLIF model successfully reproduces both constant and variable current inputs, and it was validated against the results obtained using a biophysical accurate model neuron. This enhancement provides researchers with a tool to optimize spiking neuron models using classic experimental traces under constant current injections, reliably predicting responses to synaptic inputs, which can be confidently used for large-scale network implementations. </p> <p>In order to reproduce Fig. 8 of the paper run first<br/> python AGLIF_synaptic.py<br/> in order to get the following files<br/> 6_065_voltage_simulated.txt<br/> 6_065_t_spk_simulated.txt<br/> and then run<br/> python figure8.py<br/> </p> <p> The script will produce the following image<br/> <img src="figure8_2.png" alt="Figure 8"> </p> <p>Under Ubuntu unix systems:<br/> install cmake and build-essential:<br/> sudo apt install cmake<br/> sudo apt-get install build-essential<br/> install anaconda3 following instructions from:<br/> ...<br/> <p> </p>Create a Conda Enviroment following instructions at https://github.com/nest/nest-simulator/blob/master/environment.yml OR<br/> create a conda environment:<br/> conda create -n nest python=3.9<br/> conda activate nest<br/> <br/> install the following packages:<br/> conda install -c anaconda numpy<br/> conda install -c forge matplotlib<br/> conda install -c conda-forge openmpi<br/> conda install -c anaconda gsl<br/> conda install -c anaconda cython<br/> <br/> to compile the NEST simulator with our AGLIF model:<br/> download the correct nest version using:<br/> git clone https://github.com/nest/nest-simulator.git<br/> git fetch<br/> git checkout 01f6e5a763906a3b7cf6713b887366af7bc20a44<br/> <br/> Apply the patch:<br/> git apply patch_ModelDB_synaptic_paper.patch<br/> <br/> mkdir ../nest-build<br/> cd ../nest-build<br/> cmake ../nest-simulator<br/> make<br/> make install<br/> <br/> To run the simulation put these files in a new directory:<br/> membranepot_trace_l23-06-13.res.6-tt6clu2_0.65+1_prova06122022.txt<br/> run_mds_nest.py<br/> AGLIF_synaptic_model_MARASCO_et_al.py<br/> and run:<br/> conda activate nest<br/> python AGLIF_synaptic_model_MARASCO_et_al<br/> new files will be generated:<br/> spikes.txt<br/> membranepot_trace_l23-06-13.res.6-tt6clu2_0.65+1_prova06122022.txt<br/> Model_traces_for_constant_current_injections_NEST.png<br/> that can be compared with the files generated by us with the same filenames found in the compressed file:<br/> marasco_etal.zip<br/> </p> <p>Questions on how to use this model<br/> should be directed to michele.migliore at cnr.it<br/> Questions on how to modifiy or run this<br/> model should be addressed to smgsolinas at uniss.it<br/> </p> <hr> <p> Curator's Note (2024-05-05):<br> <br> Depending on where you downloaded this from, you may find two zip files in the <code>marasco_etal</code> folder and one at the top level. If so, these should be expanded before running the code. </p> </body> </html>
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Modeling realistic synaptic inputs of CA1 hippocampal pyramidal neurons and interneurons via Adaptive Generalized Leaky Integrate-and-Fire models (Marascoa et al., 2024)