├── .coverage ├── .coveragerc ├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── Makefile ├── api.rst ├── cli.rst ├── conf.py ├── generate_recordings.rst ├── generate_templates.rst ├── images │ ├── overview.png │ ├── recordings_static.png │ ├── summary.png │ └── templates_drift.png ├── index.rst ├── installation.rst ├── make.bat ├── overview.rst ├── requirements.txt ├── usage.rst └── whatisnew.rst ├── figures ├── figure1.py ├── figure3.py ├── figure4.py ├── figure5.py ├── figure5_params.yaml ├── figure6.py ├── figure6_params.yaml ├── figure7.py ├── figure7_params.yaml ├── figure8.py ├── figure8_params.yaml ├── performance.py └── plotting_conventions.py ├── notebooks ├── generate_neuropixels_templates_and_recordings.ipynb ├── generate_recordings_with_allen_models.ipynb ├── generate_recordings_with_user_defined_spiketrains.ipynb ├── generate_recordings_with_varying_bursting_modulation.ipynb ├── generate_templates_and_recordings.ipynb ├── generate_templates_and_recordings_drift.ipynb ├── generate_templates_and_recordings_int16.ipynb ├── generate_templates_and_recordings_on_multiple_probes.ipynb └── generate_varying_noise_levels.ipynb ├── pyproject.toml ├── readthedocs.yml └── src └── MEArec ├── __init__.py ├── cell_models └── bbp │ ├── L5_BP_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── C240300C1_-_Scale_x1.000_y1.050_z1.000_-_Clone_17.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_BTC_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── C160998B-I_-_Scale_x1.000_y1.050_z1.000_-_Clone_5.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_ChC_cACint209_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── C091000D-I3_-_Scale_x1.000_y1.025_z1.000_-_Clone_6.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_DBC_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── rp100428-12_idC_-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_LBC_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── og061123b1-3_idB_-_Scale_x1.000_y0.975_z1.000_-_Clone_4.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_MC_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── C040601.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_NBC_bAC217_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── C080301B1_-_Scale_x1.000_y1.050_z1.000_-_Clone_2.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_NGC_bNAC219_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── rp110125_L5-2_idA_-_Scale_x1.000_y0.950_z1.000_-_Clone_42.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_SBC_bNAC219_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── Ca.mod │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── og061106a1_idA_-_Scale_x1.000_y1.050_z1.000_-_Clone_5.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_STPC_cADpyr232_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── dend-C231296A-P3_axon-C231296A-P3_-_Clone_9.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_TTPC1_cADpyr232_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── dend-C060114A2_axon-C060114A5.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ ├── L5_TTPC2_cADpyr232_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── dend-C060114A7_axon-C060116A3_-_Clone_2.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc │ └── L5_UTPC_cADpyr232_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ ├── CaDynamics_E2.mod │ ├── Ca_HVA.mod │ ├── Ca_LVAst.mod │ ├── Ih.mod │ ├── Im.mod │ ├── K_Pst.mod │ ├── K_Tst.mod │ ├── NaTa_t.mod │ ├── NaTs2_t.mod │ ├── Nap_Et2.mod │ ├── ProbAMPANMDA_EMS.mod │ ├── ProbGABAAB_EMS.mod │ ├── SK_E2.mod │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ └── dend-Fluo15_left_axon-Fluo15_left_-_Scale_x1.000_y0.950_z1.000_-_Clone_30.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ ├── mtype_map.tsv │ ├── synapses.hoc │ ├── synapses.tsv │ └── synconf.txt │ └── template.hoc ├── cli.py ├── 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