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Compute impedance profile from chirp current-clamp protocol #365

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Merged
JCorson merged 9 commits into from
May 12, 2026
Merged

Compute impedance profile from chirp current-clamp protocol #365

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8e2c263
feat(analysis): add impedance-profile analysis from chirp current-cla…
JCorson May 11, 2026
3843057
feat(ui): add dedicated impedance-analysis view for the Chirp protocol
JCorson May 11, 2026
4d55f58
fix(analysis): only report chirp impedance for subthreshold responses
JCorson May 11, 2026
61ef327
feat(analysis): recover impedance from spike-free chirp sub-windows
JCorson May 11, 2026
82eedc8
feat(ui): surface impedance unavailability reason and sub-window caption
JCorson May 11, 2026
a93ac36
feat(presets): tune FREQUENCY_RESPONSE so the chirp runs out of the box
JCorson May 11, 2026
58242e5
test: cover spike-free sub-window fallback and tuned FREQUENCY_RESPONSE
JCorson May 11, 2026
9c6c27c
fix(analysis): report impedance resonance only when f_R/Q/peak are al…
JCorson May 12, 2026
c321979
refactor(analysis): tighten impedance analysis per code review
JCorson May 12, 2026
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10 changes: 10 additions & 0 deletions patch_sim/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
GVAnalysisResult,
GVPoint,
HyperpolarizationAnalysisResult,
ImpedanceProfile,
IVAnalysisResult,
IVPoint,
PassiveProperties,
Expand All @@ -39,6 +40,7 @@
analyze_calcium_transients_from_result,
analyze_fi,
analyze_hyperpolarization,
analyze_impedance,
analyze_iv,
analyze_passive_properties,
analyze_sfa,
Expand All @@ -54,7 +56,9 @@
density_to_absolute_r_in,
double_exp_decay,
estimate_rheobase,
impedance_unavailable_reason,
is_subthreshold,
longest_subthreshold_run,
run_membrane_test,
single_exp_decay,
single_exp_rise,
Expand All @@ -69,6 +73,7 @@
simulate_voltage_clamp_from_state,
)
from .constants import (
CHIRP_PROTOCOL,
CURRENT_CLAMP,
CURRENT_PROTOCOLS,
DEFAULT_Q10,
Expand Down Expand Up @@ -118,6 +123,7 @@
"GVAnalysisResult",
"GVPoint",
"HyperpolarizationAnalysisResult",
"ImpedanceProfile",
"IVAnalysisResult",
"IVPoint",
"PassiveProperties",
Expand All @@ -135,6 +141,7 @@
"analyze_calcium_transients_from_result",
"analyze_fi",
"analyze_hyperpolarization",
"analyze_impedance",
"analyze_iv",
"analyze_passive_properties",
"analyze_sfa",
Expand All @@ -150,10 +157,13 @@
"density_to_absolute_r_in",
"double_exp_decay",
"estimate_rheobase",
"impedance_unavailable_reason",
"is_subthreshold",
"longest_subthreshold_run",
"run_membrane_test",
"single_exp_decay",
"single_exp_rise",
"CHIRP_PROTOCOL",
"CURRENT_CLAMP",
"CURRENT_PROTOCOLS",
"DEFAULT_Q10",
Expand Down
11 changes: 11 additions & 0 deletions patch_sim/analysis/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
derivatives: General-purpose derivative utilities (e.g. dV/dt).
fi_curve: F-I curve construction from current clamp multi-sweep results.
hyperpolarization: Sag and rebound analysis from hyperpolarization sweeps.
impedance: Impedance-profile analysis from a chirp current-clamp run.
iv_curve: I-V curve construction from voltage clamp multi-sweep results.
membrane_test: Dedicated membrane test for passive property characterisation.
passive_properties: Passive membrane property extraction (R_in, τₘ, Cₘ).
Expand Down Expand Up @@ -55,6 +56,11 @@
analyze_hyperpolarization,
compute_sag_point,
)
from .impedance import (
ImpedanceProfile,
analyze_impedance,
impedance_unavailable_reason,
)
from .iv_curve import IVAnalysisResult, IVPoint, analyze_iv, compute_iv_point
from .membrane_test import (
MEMBRANE_TEST_CURRENT,
Expand All @@ -69,6 +75,7 @@
density_to_absolute_c_m,
density_to_absolute_r_in,
is_subthreshold,
longest_subthreshold_run,
)
from .sfa import SFAAnalysisResult, SFACurve, analyze_sfa, compute_sfa
from .tau_v import (
Expand All @@ -92,6 +99,7 @@
"analyze_calcium_transients_from_result",
"analyze_fi",
"analyze_hyperpolarization",
"analyze_impedance",
"analyze_iv",
"analyze_passive_properties",
"analyze_sfa",
Expand All @@ -108,7 +116,9 @@
"density_to_absolute_r_in",
"double_exp_decay",
"estimate_rheobase",
"impedance_unavailable_reason",
"is_subthreshold",
"longest_subthreshold_run",
"run_membrane_test",
"single_exp_decay",
"single_exp_rise",
Expand All @@ -123,6 +133,7 @@
"FIAnalysisResult",
"FIPoint",
"HyperpolarizationAnalysisResult",
"ImpedanceProfile",
"SagPoint",
"GVAnalysisResult",
"GVPoint",
Expand Down
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