From b5fe0c7e7b186655e709400de97b68e991cf65bc Mon Sep 17 00:00:00 2001 From: Michael Clerx Date: Fri, 11 Oct 2024 12:07:56 +0200 Subject: [PATCH 1/2] Update README.md --- artefacts/README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/artefacts/README.md b/artefacts/README.md index 341416c..143aa02 100644 --- a/artefacts/README.md +++ b/artefacts/README.md @@ -23,4 +23,9 @@ In the second notebook we update the model to include the compensation circuitry In notebook number four we derive simplified models of the compensated voltage clamp setup, which can be used in fitting. +## Appendices +- Electronics + - A1. Ideal op amps [![github](../img/github.svg)](appendix-A1-op-amp.ipynb) + - A2. Laplace transforms and filters [![github](../img/github.svg)](appendix-A2-laplace-and-filters.ipynb) + - A3. Non-ideal op amps [![github](../img/github.svg)](appendix-A3-non-ideal-op-amp.ipynb) From 01979d390c5a62f2eab0fecf6f8e117e4c712a18 Mon Sep 17 00:00:00 2001 From: Michael Clerx Date: Fri, 11 Oct 2024 13:01:44 +0200 Subject: [PATCH 2/2] Update README.md --- artefacts/README.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/artefacts/README.md b/artefacts/README.md index 143aa02..b692dcf 100644 --- a/artefacts/README.md +++ b/artefacts/README.md @@ -1,4 +1,3 @@ - # Modelling patch-clamp experiments When analysing data from whole-cell patch-clamp experiments, it can be useful to have a model of both the biological system of interest _and_ the experimental set up. @@ -29,3 +28,20 @@ In notebook number four we derive simplified models of the compensated voltage c - A1. Ideal op amps [![github](../img/github.svg)](appendix-A1-op-amp.ipynb) - A2. Laplace transforms and filters [![github](../img/github.svg)](appendix-A2-laplace-and-filters.ipynb) - A3. Non-ideal op amps [![github](../img/github.svg)](appendix-A3-non-ideal-op-amp.ipynb) +- Extended models + - B1. Models without compensation [![github](../img/github.svg)](appendix-B1-uncompensated-models.ipynb) + - B2. Models with compensation [![github](../img/github.svg)](appendix-B2-compensated-models.ipynb) + - B3. Sigworth 1983/1995 Rs compensation [![github](../img/github.svg)](appendix-B3-sigworth-rs.ipynb) +- Parameter names and values + - C1. Names & symbols [![github](../img/github.svg)](appendix-C1-symbols.ipynb) + - C2. Default parameter values used in examples [![github](../img/github.svg)](appendix-C2-parameter-defaults.ipynb) + - C3. Parameter values, estimates for different amplifiers etc. [![github](../img/github.svg)](appendix-C3-parameter-values.ipynb) +- Remaining noise and errors + - D1. Strategies for dealing with experimental error [![github](../img/github.svg)](appendix-D1-strategies.ipynb) + - D2. Stochastic and periodic noise [![github](../img/github.svg)](appendix-D2-inspecting-noise.ipynb) + - D3. Liquid junction potential [![github](../img/github.svg)](appendix-D3-liquid-junction-potential.ipynb) + - D4. Leak (unfinished) [![github](../img/github.svg)](appendix-D4-leak.ipynb) + - D5. Handling remaining capacitance artefacts (unfinished) [![github](../img/github.svg)](appendix-D5-remaining-Cp-artefacts.ipynb) +- Estimating Rs and Cm + - E1. Estimating Rs and Cm; a one-shot approach [![github](../img/github.svg)](appendix-E1-rs-cm-one-shot.ipynb) + - E2. Estimating Rs and Cm; an iterative approach [![github](../img/github.svg)](appendix-E2-rs-cm-iterative.ipynb)