Working on filters

Author: MichaelClerx

artefacts/NOISE.ipynb

@@ -0,0 +1,44 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "86649012-4219-45f8-a42b-2f222159d7c9",
+   "metadata": {},
+   "source": [
+    "\n",
+    "\n",
+    "- Look at noise notebook again\n",
+    "- Look at pink noise:\n",
+    "  - Can we tell from spectrum what \"color\" the noise is?\n",
+    "  - \"Pink noise\" looks interesting\n",
+    "  - https://stackoverflow.com/questions/67085963/generate-colors-of-noise-in-python\n",
+    "  - https://en.wikipedia.org/wiki/Pink_noise\n",
+    "  - https://en.wikipedia.org/wiki/Johnson%E2%80%93Nyquist_noise\n",
+    "- Look at shot noise:\n",
+    "  - Looks interesting: https://electronics.stackexchange.com/questions/716039/noise-in-classical-quantum-transmission\n",
+    "  - But what time scale does this happen on?"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

artefacts/appendix-A4-bessel-filters.ipynb

@@ -1452,7 +1452,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
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artefacts/appendix-A5-bessel-filter-odes.ipynb

@@ -1026,7 +1026,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.13.2"
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artefacts/appendix-B1-uncompensated-models.ipynb

@@ -926,9 +926,9 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.13.2"
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- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

artefacts/appendix-D2-inspecting-noise.ipynb

@@ -64,8 +64,14 @@
    "source": [
     "## How do we calculate the LJP?\n",
     "\n",
-    "In short, almost everyone uses [a piece of software developed by Peter Barry](https://doi.org/10.1016/0165-0270(94)90031-0). \n",
-    "An [open source alternative](https://swharden.com/LJPcalc/) based on a newer model is also available, as described in [Marino et al. 2014](https://arxiv.org/abs/1403.3640)."
+    "The LJP can be estimated based on the concentrations of free charged molecules in the bath and pipette solution.\n",
+    "Most commonly, [a piece of software developed by Peter Barry](https://doi.org/10.1016/0165-0270(94)90031-0) is used, but an [open source alternative](https://swharden.com/LJPcalc/) based on a more accurate model is also available, as described in [Marino et al. 2014](https://arxiv.org/abs/1403.3640).\n",
+    "\n",
+    "An added difficulty here is that the solutions given in methods sections are always _total concentrations_, not _free concentrations_.\n",
+    "In particular:\n",
+    "- Ca, Mg (and others) are buffered by EGTA, ATP (and others). Free concentrations are typically orders of magnitude lower than total concentrations (added mM of Ca2+ become uM after buffering). They can be estimated using problems like [MaxChelator](https://somapp.ucdmc.ucdavis.edu/pharmacology/bers/maxchelator/index.html).\n",
+    "- pH adjustment of solution is typically done with XOH, where X is Na, K, Cs or some other ion. The exact amount is not usually mentioned in methods sections, but can affect the final solutions.\n",
+    "- pH regulators like HEPES bind or release H+ (H-Hepes <--> H+ + HEPES-), which may need to be taken into account."
    ]
   },
   {
@@ -243,7 +249,7 @@
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    "pygments_lexer": "ipython3",
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artefacts/appendix-D3-liquid-junction-potential.ipynb

@@ -856,7 +856,7 @@
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artefacts/artefacts-1-modelling-patch-clamp.ipynb

@@ -343,6 +343,46 @@
     "where typical values for $\\tau_\\text{sum}$ are $2\\mu s$ (fast), $10\\mu s$ (average), or $100\\mu s$ (slow, see [Appendix C3](./appendix-C3-parameter-values.ipynb))."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3f4a712d-9dd5-48d9-96c7-f85ad55bf365",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f67c7146-8f3f-42bc-b329-138f53fe4342",
+   "metadata": {},
+   "source": [
+    "\\begin{align}\n",
+    "V_\\text{ref} = V_c + \\alpha R_s^* I_\\text{obs} + \\beta R_s^* C_m^* \\dot{V}_\\text{est}\n",
+    "\\end{align}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9e06a285-6e73-4b2f-820e-e6e07088e9df",
+   "metadata": {},
+   "source": [
+    "\\begin{align}\n",
+    "V_\\text{ref} = V_c + V_s + \\beta R_s^* C_m^* \\dot{V}_\\text{est}\n",
+    "\\end{align}\n",
+    "\n",
+    "\\begin{align}\n",
+    "\\tau_s \\dot{V_s} = \\alpha R_s^* I_\\text{obs} - V_s\n",
+    "\\end{align}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "31c5c489-1d08-41bd-af28-cf8843a1df6d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "id": "934470f3",
@@ -642,7 +682,7 @@
     "4. Series resistance correction\n",
     "5. Series resistance prediction\n",
     "\n",
-    "In the next notebook we will run simulations to investigate the model in detail."
+    "In the next notebook we will discuss _filtering_ of the input and output signals."
    ]
   }
  ],
@@ -662,7 +702,7 @@
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