Nanion Patchliner Analysis Toolkit

An Igor Pro procedure package for analysis of automated patch clamp data acquired with the Nanion Patchliner system using PatchMaster software.

Targets the electrophysiology research community. Intended for submission to IgorExchange (WaveMetrics community platform).

---

Requirements

• Igor Pro 8 or later
• Data acquired with Nanion Patchliner / PatchMaster (exported as Igor binary waves)

---

Installation

1. Copy all .ipf files into your Igor Pro User Procedures folder
   (Igor Pro User Files/User Procedures/)
2. In Igor Pro: File → Open File → Procedure, open Analysis_Menus.ipf
   (remaining modules are included automatically via #include — pending)
3. From the menu bar: Analysis → Nanion → Panel

---

Quick Start

1. Load your PatchMaster-exported waves into Igor Pro
2. Open the toolkit: Analysis → Nanion → Panel
3. In the Organize tab: click Organize data and enter your wave prefix
   (e.g. Cell for waves named Cell_001, Cell_002, …)
4. Navigate to an experiment folder and select the appropriate protocol tab
5. Use the Export tab to send data to NeuroMatic for further analysis

---

Module Structure

File	Responsibility
Analysis_Menus.ipf	Entry point, main panel, tab control, menu functions
Analysis_Utils.ipf	Logger, global variable helpers, folder path helpers, wave utilities, graph window helpers
Analysis_Common.ipf	Signal preprocessing, wave organization (sorting_hat), passive property estimation (pasivas)
Analysis_Ramp.ipf	Ramp protocol analysis (tempresponse)
Analysis_IV.ipf	IV protocol analysis (AnalizarIVporCanal), IV and raw trace graphs
Analysis_Amplitude.ipf	Amplitude extraction from ramp fits, result wave management, cursor hook
Analysis_IVCurves.ipf	Reversal potential, chord conductance, G-V curve, Boltzmann fit, IV normalization
Analysis_Kinetics.ipf	Temperature-dependent kinetics: Q10 and Arrhenius analysis
Analysis_NMExport.ipf	NeuroMatic export: copies all Patchliner channels into a single NM-compatible folder

---

Folder Hierarchy

After running Organize data, waves are moved into the following structure:

root:
└── chan_X:                    ← per channel (e.g. chan_A, chan_B)
    ├── Packages:              ← channel globals (Wave_prefix, chanexp)
    ├── Ramp_Analysis:         ← result waves for ramp protocol
    ├── IV_Analysis:           ← result waves for IV protocol
    └── exp_Y:                 ← per experiment
        ├── Trace:             ← current traces
        ├── Stim:              ← stimulus amplitude and duration waves
        ├── Packages:          ← experiment globals (ramp_temp, etc.)
        └── Analysis:          ← intermediate analysis waves

Folder management rules

Rule	Description
R1	Administrative folders (Packages, Trace, Stim) — created by sorting_hat / prefix_detector only
R2	Intermediate folders (exp_Y:Analysis:) — created by the analysis function that needs them
R3	Result folders (chan_X:Ramp_Analysis:, chan_X:IV_Analysis:) — created by CheckDataFolder on first use
R4	Path resolution — functions receive folder paths as parameters; no internal resolution
R5	exp_type as explicit parameter — no function detects protocol type automatically

---

Analysis Workflows

Ramp protocol

prefix_detector()          → organize waves into folder hierarchy
plot_raw_panel()           → visualize traces and stimulus
menu_tempresponse()        → baseline fit + peak extraction + passive properties
plot_amp("raw")            → amplitude panel with cursor-based selection

Result waves (in chan_X:Ramp_Analysis:):

Wave	Columns	Units
MutantName_Prefix_Chan_Amp	[0] baseline, [1] peak, [2] delta	pA
chan_fitpeak_T	[0] mode 0 (linear fit), [2] mode 2 (no fit)	same as input
chan_pasives_T	[0] Cm, [1] tau, [2] Rs	pF, ms, MΩ

IV protocol

prefix_detector()          → organize waves
AnalizarIVporCanal()       → current, voltage, passive properties per sweep
IV_graph()                 → current vs voltage plot

Result wave IV_Results (in exp_Y:Analysis:):

Column	Quantity	Unit
[0]	Current	A
[1]	Voltage	V
[2]	Cm	F
[3]	tau	s
[4]	Rs	Ω

IV curves (from IV_Results)

reversal_potential_fit(IV_res, Rs_corr)   → V_rev by zero-crossing interpolation
conductance_calc(IV_res, V_rev_mV)        → chord conductance G = I / (V - V_rev)
GV_curve(G_chord, IV_res)                 → normalized G-V: G_norm = G / G_max
boltzmann_fit(GV_norm, IV_res, pkg_folder)→ V_half and slope k
IV_normalize(IV_res)                       → normalized IV curve

---

NeuroMatic export

prefix_detector()          → organize waves into folder hierarchy
ExportChannelToNM()        → export all Patchliner channels to a single NM folder

Maps each chan_X folder to a NeuroMatic channel letter (alphabetical order):

Patchliner channel	NM channel
chan_1	A
chan_2	B
chan_3	C
chan_4	D

All waves are copied — the source folder structure is preserved. Experiments within each channel are sorted alphabetically so wave sequence numbers are stable across runs.

Output folder at root: nm_{expName}

Stimulus export (voltage command reconstruction from _Amp/_Dur pairs) is pending.

---

Key Design Conventions

Cursor / active wave tracking

Every graph that uses cursors for analysis stores the active wave's full path in:

root:Packages:[graph_name]_wave_path

obtained via GetWavesDataFolder(w, 2). This is required because CsrWave() does not work reliably with hosted subgraphs (# syntax). The path is consumed by CursorMovedHook and button procedures.

Global variable sentinel

nvar_storer(name, value, folder) uses NaN as the retrieve-mode sentinel, so legitimate stored zero values are preserved correctly.

Cursor placement

All cursor placement uses /P (point-based) flags to avoid XY-axis scaling mismatches.

---

Analytical Methods

Passive properties (Molleman 2003)

Estimated from the capacitive transient in response to a voltage step:

Rs   = ΔV / I₀         (I₀ = peak current at step onset)
Rtot = ΔV / Iss        (Iss = steady-state current)
Rm   = Rtot − Rs
τ    = RC fit time constant
Cm   = τ / Rpar        (Rpar = Rs ∥ Rm)

Chord conductance (Bhatt et al. 2017 PLOS ONE)

G(V) = I(V) / (V − V_rev)      [nA/mV = µS]

Reversal potential (Scenario 2 — experimental)

Linear interpolation at the zero-current crossing of the IV curve, with optional Rs correction following Beyder & Bhargava 2021 Sci Rep.

Boltzmann fit

G_norm(V) = 1 / (1 + exp((V_half − V) / k))

Q10 temperature coefficient

Q10 = (A_j / A_i) ^ (10 / (T_j − T_i))

Arrhenius activation energy

ln(A) = ln(A₀) − Ea / (R · T)      →      Ea (kJ/mol) = −slope × R

R = 8.314 J/(mol·K); linear fit of ln(amplitude) vs 1/T (K⁻¹).

---

References

• Molleman A (2003). Patch Clamping: An Introductory Guide to Patch Clamp Electrophysiology. Wiley.
• Bhatt DL et al. (2017). Chord conductance analysis in Nanion SyncroPatch. PLOS ONE.
• Beyder A & Bhargava A (2021). Series resistance errors in whole-cell recordings. Scientific Reports.
• Zgrablic G et al. (2020). Patch clamp with temperature control on Patchliner. Bioengineering.

---

Development Status

Feature	Status
Wave organization (sorting_hat)	✅ Complete
Ramp analysis (tempresponse)	✅ Complete
Amplitude extraction	✅ Complete
IV analysis (AnalizarIVporCanal)	✅ Complete
IV curves — Scenario 2 (experimental V_rev)	✅ Complete
IV curves — Scenario 1 (Nernst/GHK V_rev)	🔲 Stub
IV curves — Scenario 3 (blocker conditions)	🔲 Stub
Q10 / Arrhenius kinetics	⚠️ Functional, under review
Ramp mode 1 (fit near 0 mV)	🔲 TODO
NeuroMatic export — current traces (Ch A–D)	⚠️ Functional, under review
NeuroMatic export — voltage command reconstruction	🔲 Pending
nT, t0, dt from Packages globals	🔲 TODO (currently hardcoded in amp_saver)
IPT lint + format pass	🔲 Before IgorExchange submission
#include wiring between modules	🔲 Before IgorExchange submission

---

Known Limitations

• Timing parameters in AnalizarIVporCanal() and tempresponse() are hardcoded for the current Nanion Patchliner square-pulse and ramp protocols. Adaptation to other protocols requires manual adjustment.
• nT, t0, dt (temperature grid) are hardcoded as 6, 20, 5 in amp_saver() and amp_retreiver(). Will be refactored to read from Packages globals before publication.
• Arrhenius_calculator() fit range is hardcoded to indices [2, 4].

---

License

To be defined prior to IgorExchange submission.