crash: move images

Author: swharden

content/crash/ap/index.md renamed to content/crash/ap.md

@@ -7,7 +7,7 @@ weight: 50
 When the action potential threshold voltage is reached, an action potential ensues. Action potentials can occur spontaneously either because the neuron naturally rests above its threshold (in which case it fires continuously), or because excitatory synaptic inputs (EPSPs) raise its voltage above threshold.
 
 <figure class="figure">
-  <img src="spontaneous-action-potential.png" class="figure-img img-fluid rounded">
+  <img src="/patch/img/crash/ap/spontaneous-action-potential.png" class="figure-img img-fluid rounded">
   <figcaption class="figure-caption">
 
 **Action Potentials in Current-Clamp Configuration.** Sub-threshold EPSPs are visible in this example. When EPSPs are sufficiently large (or enough EPSPs occur simultaneously), the neuron is depolarized past action potential threshold and an action potential ensues.
@@ -18,7 +18,7 @@ When the action potential threshold voltage is reached, an action potential ensu
 Action potentials can be incited by current delivered through the patch pipette. In this case, the current delivered is commonly displayed below the current-clamp recording trace.
 
 <figure class="figure">
-  <img src="step-aps.png" class="figure-img img-fluid rounded">
+  <img src="/patch/img/crash/ap/step-aps.png" class="figure-img img-fluid rounded">
   <figcaption class="figure-caption">
 
 **Excitatory current delivered through the recording pipette evokes action potentials.** One second pulses of excitatory current delivered through the recording pipette (bottom traces) depolarizes this neuron past its AP threshold and results in a continuous train of action potentials (top traces). The greater the excitatory current delivered, the faster the action potentials fire. The relationship between current injection and the resulting frequency of action potentials is commonly referred to as action potential gain.

content/crash/how/index.md renamed to content/crash/how.md

@@ -7,7 +7,7 @@ description: Steps for establishing whole-cell patch-clamp configuration with ne
 
 Your chances of achieving successful patches increase if you do a good job at targeting healthy neurons. Quality neurons appear flat and have crisp borders. Smaller shriveled neurons (which often look more 3D than the rest) are typically sick.
 
-<img src="dic-neuron.png" class="img-fluid my-5 w-75 d-block mx-auto shadow">
+<img src="/patch/img/crash/how/dic-neuron.png" class="img-fluid my-5 w-75 d-block mx-auto shadow">
 
 Figure: Examples of good (green) and bad (red) neurons for patching. This example image uses DIC optics and was taken in the CA1 layer of the rat hippocampus.
 
@@ -17,25 +17,25 @@ Figure: Examples of good (green) and bad (red) neurons for patching. This exampl
 
 Apply positive pressure by blocking the exit path and pressing the plunger.
 
-<img src="syringe-1.png" class="img-fluid w-50 mx-auto d-block">
+<img src="/patch/img/crash/how/syringe-1.png" class="img-fluid w-50 mx-auto d-block">
 
 ### Suction
 
 Before applying suction open the exit path to allow positive pressure to escape. Then block the exit path and lift the plunger slightly.
 
-<img src="syringe-2.png" class="img-fluid w-50 mx-auto d-block">
+<img src="/patch/img/crash/how/syringe-2.png" class="img-fluid w-50 mx-auto d-block">
 
 ### Zero Pressure
 
 Open the exit path to equalize pressure.
 
-<img src="syringe-3.png" class="img-fluid w-25 mx-auto d-block">
+<img src="/patch/img/crash/how/syringe-3.png" class="img-fluid w-25 mx-auto d-block">
 
 # Steps to Patch a Cell
 
 The borosilicate glass of the patch pipette will stick to the first lipophilic substance it touches, so it is critical that the first thing to contact the inside the tip is the membrane of the neuron to be patched.
 
-<img src="steps.png" class="img-fluid d-block mx-auto">
+<img src="/patch/img/crash/how/steps.png" class="img-fluid d-block mx-auto">
 
 ## Step 1: Approach
 
@@ -45,7 +45,7 @@ The goal of this step is to move the pipette near the target cell. Positive pres
 
 - **Zero the pipette offset:** Click the `bath` button, press ⏸, and the line should go flat. Now click 🔓 and `auto`, and the line should be centered at zero. Click the ▶ button and a square shape should appear.
 
-<img src="memtest-bath.png" class="img-fluid w-50 mx-auto d-block shadow my-5">
+<img src="/patch/img/crash/how/memtest-bath.png" class="img-fluid w-50 mx-auto d-block shadow my-5">
 
 ## Step 2: Seal
 
@@ -55,11 +55,11 @@ The goal of this step is to suck a small piece of membrane into the tip so it fo
 
 - Push the pipette tip into the cell until you see a growing _dimple_ expanding indicating that the pipette is pressed into the cell
 
-<img src="patch.gif" class="img-fluid d-block mx-auto shadow-sm my-3">
+<img src="/patch/img/crash/how/patch.gif" class="img-fluid d-block mx-auto shadow-sm my-3">
 
 - Quickly release pressure, apply slight suction, click the `patch` button, and allow the seal to form. A quality seal is marked by the line quickly becoming flat and the reading indicating R<sub>t</sub> is >1 GΩ
 
-<img src="memtest-patch.png" class="img-fluid w-50 mx-auto d-block shadow my-5">
+<img src="/patch/img/crash/how/memtest-patch.png" class="img-fluid w-50 mx-auto d-block shadow my-5">
 
 ## Step 3: Break
 
@@ -71,4 +71,4 @@ The goal of this step is to suck a small piece of membrane into the tip so it fo
 
 - Click the `cell` button to evaluate access resistance (Ra). Apply additional suction in short bursts as needed to ensure Ra is as low as possible (typically around 20 MΩ).
 
-<img src="memtest-cell.png" class="img-fluid w-50 mx-auto d-block shadow my-5">
+<img src="/patch/img/crash/how/memtest-cell.png" class="img-fluid w-50 mx-auto d-block shadow my-5">

content/crash/intro/index.md renamed to content/crash/intro.md

@@ -18,15 +18,15 @@ Patch-clamp technique can be used to measure the electrical properties of indivi
 
 The artificial cytoplasm (called **pipette solution** or **internal solution**) contains molecules typically found inside a neuron (K<sup>+</sup>, Ca<sup>2+</sup>, Ca<sup>2+</sup> buffer, ATP, GTP, etc.). Experiments are performed on brain slices submerged an **extracellular solution** consisting of oxygenated artificial cerebrospinal fluid (**ACSF**) containing molecules typically found in CSF (Cl<sup>-</sup>, Na<sup>+</sup>, buffering agents, etc.). 
 
-<img src="whole-cell.png" class="d-block mx-auto my-4 img-fluid">
+<img src="/patch/img/crash/intro/whole-cell.png" class="d-block mx-auto my-4 img-fluid">
 
 > 💡 An easy way to remember which ions are inside vs. outside neurons is to recall that neurons evolved in the ocean, so the major ions in salt water (Na<sup>+</sup> and Cl<sup>-</sup>) are in high concentrations _outside_ the neuron. Other ions (largely K<sup>+</sup>) exist at higher concentrations _inside_ the neuron.
 
 ## Ion Channels and the Cell Membrane
 
 What is actually being studied when a neuron is recorded? Since patch-clamp recordings measure the electrical difference between intracellular vs. extracellular solutions, what gets measured is just the thing that separates the two: the **cell membrane**. When we use patch-clamp technique characterize the electrical properties of a neuron, we really reporting the electrical properties of the _membrane_ that forms the cell we are puncturing.
 
-<img src="bilayer.png" class="d-block mx-auto my-4 rounded img-fluid border border-dark shadow">
+<img src="/patch/img/crash/intro/bilayer.png" class="d-block mx-auto my-4 rounded img-fluid border border-dark shadow">
 
 **Resistance** is the degree to which a material _resists_ the flow of ions. Since cell membranes are largely made of phospholipid bilayers, **cell membranes have a high resistance**. This means they do not readily permit the passage of ions without the help of membrane-embedded proteins that serve as channels for charged molecules (ions). Neural membranes contain large numbers of **ion channels** which act like little holes in the membrane and permit the flow of particular ions in or out of the neuron, reducing the membrane resistance while the channels are open. The inverse of resistance is **conductance**, and opening ion channels in the neural membrane increases conductance (and decreases resistance). There is a wide variety of ion channels, and they typically vary by what ions they pass (influencing whether they are excitatory or inhibitory) and what controls their open state (always open, gated by voltage, and/or gated by ligand binding).
 

content/crash/ohms-law/index.md renamed to content/crash/ohms-law.md

@@ -12,7 +12,7 @@ Patch-clamped neurons can be used to measure spontaneous currents that result fr
 
 ## Pre-Synaptic vs. Post-Synaptic
 
-<img src="synaptic-neuron.png" class="d-block mx-auto img-fluid">
+<img src="/patch/img/crash/synaptic-currents/synaptic-neuron.png" class="d-block mx-auto img-fluid">
 
 Synapses are the chemical connection between an upstream (pre-synaptic) and downstream (post-synaptic) neuron. When the pre-synaptic neuron fires an action potential (AP), neurotransmitter is released from the axon terminal. In this example, the neurotransmitter is excitatory. When the neurotransmitter acts on the post-synaptic neuron (the neuron being recorded), the excitatory action of that synapse is observed as an excitatory post-synaptic current. Although this method only directly measures currents in the post-synaptic neuron, the frequency of post-synaptic currents is related to the frequency of pre-synaptic action potential firing.
 
@@ -31,8 +31,8 @@ One more layer of abbreviations can be added to indicate if the synaptic current
 Consider the following figure which demonstrates spontaneous excitatory and inhibitory synaptic activity in the same cell measured in voltage-clamp mode and current-clamp modes:
 
 | voltage clamp (VC) | current clamp (IC) |
-| --- | --- |
-| <img src='synaptic-vc.png' class='img-fluid'> | <img src='synaptic-ic.png' class='img-fluid'> |
+--- | ---
+<img src='/patch/img/crash/synaptic-currents/synaptic-vc.png' class='img-fluid'> | <img src='/patch/img/crash/synaptic-currents/synaptic-ic.png' class='img-fluid'>
 
 **In voltage-clamp configuration** the trace represents net membrane current. Spontaneous post-synaptic currents (EPSCs and IPSCs) are visible. IPSCs are upward deflections representing inhibitory (outward) currents. EPSCs are inward deflections representing excitatory (inward) currents. It is useful to memorize that downward deflections in voltage-clamp configuration represent inward currents and are excitatory.