+
+
+Why is impedance important?
+***********************************
+
+The figure below includes the equivalent circuit of the electrode, as discussed yesterday. The signal |Vec| must travel through the electrode, to |Vin|, the voltage before the acquisition system itself. From there, currents coming from our neurons travel to ground. They can do so either by passing through our acquisition system, or (in parallel) they can be lost to ground through shunt impedance. Shunt impedance is primarily capacitive (see section below) and represented as (|Cs|). Shunt capacitances are created by cables or the sides of electrodes; they are accidental but unavoidable capacitances in the system.
+
+.. figure:: ../media/circuit_electrode_shunt_capacitance.*
+ :align: center
+ :alt: equivalent circuit of the electrode, with a subsequent capacitance to ground representing shunt capacitance
+
+We can replace these components with a representation of the impedance (Z) they provide.
+
+.. figure:: ../media/circuit_impedance_shunt_capacitance.*
+ :align: center
+ :alt: equivalent circuit of electrode, shunt capacitance and acquisition system with each component represented as an impedance.
+
+The impedance of the shunt capacitance, |Zcs| and the impedance of the acquisition system |Za| are impedances in parallel.
+We can simplify our circuit by combining their impedances and calling it |Za|'.
+
+.. figure:: ../media/shunt_amplifier_voltage_divider.*
+ :align: center
+ :alt: The electrode impedance and the shunt+amplifier impedance in series, showing how these two parts form a voltage divider.
+
+This gives us a voltage divider, similar to the one we built before, where:
+
+.. math::
+
+ Vin = \frac{Za'}{Za'+Ze} Vec
+
+The ratio of |Ze| and |Za|' therefore determines how much of our electrode tip voltage |Vec| reaches |Vin|.
+
+**To get more of our voltage Vec into our recording system, we want to keep electrode impedance Ze low, and system input impedance Za' very high.**
+
+If |Za|’ is not substantially greater than |Ze|, |Vin| will be much lower than |Vec|. To have high |Za|’, we need amplifiers with high input impedance and high shunt impedance.
+
+Electrode Impedance
+***********************************
+
+The impedance of an electrode is a measure of its ability to resist the flow of charge across the electrode-solution interface (i.e., across the electronic conductor (metal) and ionic conductor (extracellular fluid)). It is the impedance of the whole electrode equivalent circuit we built yesterday, consisting of the resistance of the electrode metal (|Rm|) and the resistance (|Re|) and capacitance (|Ce|) of the double layer at the electrode-solution interface.
+
+.. figure:: ../media/circuit_double_layer_interface.*
+ :align: center
+
+In polarized electrodes, the large |Re| prevents much current from taking this route. Therefore, in practice, the electrode is primarily the double-layer capacitor |Ce| in series with |Rm| and |Rs| (Robinson, 1968).
+
+So far, we know that the impedance magnitude of a capacitor decreases with increased capacitance, and that electrode impedance is dominated by double layer capacitor, |Ce|. Therefore, to decrease our electrode impedance, we need to increase the electrode capacitance |Ce|.
+How can we increase the value of |Ce|?
+
+.. math::
+
+ C = \frac{\epsilon A}{d}
+
+`The capacitance of a capacitor (C, in Farads), is proportional to the area of the capacitor plates (A) divided by the distance (d) between them. ε is the electrostatic constant.`
+
+To make C bigger, we can increase the surface area (A) of the electrode, for instance by electroplating a thin layer of gold on to an electrode. We can also coat electrodes with materials complemented with pseudo-capacitance, such as conducting polymers or transition metal oxide films, such as IrOx (Green, Lovell, Wallace, & Poole-Warren, 2008; Musa, 2011).
+
+Electrode impedance magnitude is usually measured at 1 kHz, before and after electrode coating, allowing us to see an impedance decrease of up to 10-fold (Neto et al., 2018).
+
+By increasing the capacitance (|Ce|) of our electrode, the electrode impedance (|Ze|) will be smaller, preserving more of our signal amplitude at |Vin|.
+
+Shunt Impedance
+***********************************
+
+Shunt impedance is the total impedance of shunt capacitance |Cs| and shunt resistance |Rsh|. These are both routes to ground outside of the intended acquisition system. At the high frequencies (1kHz) we are interested in, the capacitive component will have relatively low impedance. It will therefore have more effect than the resistive component, so |Rsh| is often ignored.
+
+Remember that any two conducting surfaces, with a non-conducting layer in between, *is* a capacitor. Shunt capacitance arises mainly from the capacitance across the thin insulation layer isolating an electrode and the surrounding electrolyte, as well as the cumulative capacitance along cables and connectors (Robinson, 1968).
+
+The shunt capacitance for a tungsten wire (~50 to 100 pF) is usually higher than for a silicon probe (5-20 pF/cm). (Why? Think of what makes a capacitor, and the relative shape and conductances of these electrodes).
+
+.. admonition:: Try it yourself
+
+ Here is a model of the electrode with shunt capacitance, resistance, and amplifier in parallel to ground. You should see that either decreasing electrode impedance or increasing shunt impedance gives you a larger output voltage.
+
+ https://tinyurl.com/yepsdold
+
+We want a large shunt impedance, to prevent current from flowing down this route. Being capacitive, the impedance decreases with signal frequency (Nelson et al., 2008). Therefore, to create a large shunt impedance, the shunt capacitance should be small:
+
+.. math::
+ Z = \frac{1}{2 \pi fC}
+
+However, some shunt capacitance is inevitable and often there is not much we can do about it. Because the shunt impedance is in parallel with the impedance of the acquisition system, we can focus on increasing the acquisition system impedance to give us a large |Za|'.
+
+.. _refamplifierintro:
+
+Amplifiers
+#####################################################################
+
+Amplifiers in the headstage prevent current being drawn
+********************************************************************
+
+A perfect 5V voltage source would always provide exactly 5 Volts, no matter what the rest of the circuit looks like. If we put a lot of high impedance components in the rest of the circuit, less current will flow, and if we put low impedance components we will get a high current.
+
+A real voltage source has a bit of output impedance, which means it acts as a voltage source in series with an impedance. This is modelled here (click to view high-quality version in the simulator):
+
+.. figure:: ../media/output_impedance.*
+ :align: center
+ :target: https://tinyurl.com/yfvzdxbz
+ :alt: voltage sources passing a resistance to ground. Real and ideal voltage sources are compared, where real voltage sources act as a perfect voltage source in series with a small resistance.
+
+That invisible, small series resistance creates a voltage divider. Though the actual source voltage is the same 5V, the apparent voltage of the source varies depending on the ratio between the output impedance of the source, and the impedance of the rest of the circuit. The lower the impedance of the components used in the rest of the circuit, the higher the relative influence of the source output impedance, and the lower the apparent source voltage (the voltage droops).
+
+In our acquisition system, the voltage source is the potential changes in the extracellular fluid (|Vec|). The resistive and capacitive properties of the electrode create an output resistance. The relative impedance of the circuit before and after |Vin| influences the magnitude of the signal at |Vin|. If we allow a lot of current to flow from our electrode to ground, we have a low impedance circuit, which will distort our signal. We therefore need something with a very high impedance to stop current being drawn from our |Vec|. Amplifiers do exactly this: their high input impedance prevents current flow from the electrodes, and amplifiers provide the necessary current for the rest of the circuit from a separate source.
+
+The operational amplifier
+******************************************************************
+
+The `operational amplifier` or `op-amp` is a crucial building block of our acquisition system. The amplifier has two inputs (+ and -), one output, and two power rails (e.g. a 3 and -3V power rail).
+
+.. figure:: ../media/op-amp-basic.*
+ :align: center
+ :alt: an amplifier is represented as a triangle pointing towards the right. It has two inputs (+ and -) and one output.
+
+Amplifiers have high input impedance
+******************************************************************
+
+The amplifier input impedance, Z\ :sub:`a`\ is very high. The circuit acts as though the current has to cross a very high resistor to actually enter the amplifier. The current flow therefore becomes very low (Ferree et al., 2001), preventing us from drawing much current from the electrode to ground.
+
+Here is the amplifier added into our circuit diagram:
+
+.. figure:: ../media/circuit_electrode_shunt_amp.*
+ :align: center
+
+Amplifiers have low output impedance
+******************************************************************
+
+The output impedance of amplifiers is very low, which means that a lot of current can flow *from* the amplifier. This current enables the driving of the signal through all the subsequent circuits (e.g., interconnect lines, multiplexer, and ADC). By placing an amplifier in our circuit, we make sure that the rest of our recording circuit is driven by current provided by the amplifier, not by current provided by the electrode tip.
+
+Amplifiers output a voltage
+*****************************************************************
+
+The amplifier outputs the voltage difference between the voltages at its two inputs.
+
+.. figure:: ../media/op-amp-basic.*
+ :align: center
+
+How does it do that?
+
+If the difference between its two inputs is **positive**, the amplifier connects its output to the positive ‘power rail’, giving a positive output voltage. If the positive power rail is 3V, the amplifier will output (pretty much) that.
+
+If the difference between the two inputs is **negative**, the amplifier will connect its output to the negative rail, outputting -3V. While doing that, the operational amplifier draws basically no current on its inputs.
+
+In this configuration, the amplifier does not distinguish between small or large differences in voltage across its inputs; it will only every output the most negative or most positive voltage it can. Another way to say that, is that it amplifies the difference between its inputs with a huge factor, also called ‘gain’. This gain is so large that the amplifier always saturates, providing either the maximum or minimum voltage it can.
+
+Negative feedback prevents saturation
+***********************************************************
+
+.. figure:: ../media/op_amp_feedback.*
+ :align: center
+ :target: https://tinyurl.com/ygby3xqh
+ :alt: an amplifier with the output and negative terminal connected
+
+If we connect the output of the operational amplifier to the ``-`` input, then the following happens:
+
+- Initially, if ``+`` is higher than ``-``, the operational amplifier will output a high voltage.
+
+- If we connect the output back to ``-``, the amplifier will continue to output a high voltage, but now this voltage starts to increase the value of ``-``, bringing the value of the inputs closer together. This behaviour will keep the voltages at its ``+`` and ``-`` inputs the same.
+
+- Now, the ``-`` input is always actively driven to follow the voltage on the ``+`` input. This means that whatever voltage we connect to the ``+`` input can be measured just by looking at the ``-`` input (which is connected to / the same as the output). Increasing ``+`` will induce a difference between ``+`` and ``-``, but the corresponding change in the amount of output voltage will bring ``-`` back up.
+
+We can measure the voltage that at ``+`` by just measuring the output of the operational amplifier, BUT because the ``+`` input draws almost no current at all (in other words, very high input impedance), we can now measure weak signals. The output of the operational amplifier on the other hand side has very low output impedance. In other words, we can draw a lot of current from it and it will keep its voltage.
+
+You can run this example in the simulator (click the image above), and see if what we said about the operational amplifier makes sense.
+
+An op-amp as a headstage
+**********************************************************
+
+Our electrodes will be attached to a headstage, which contains an amplifier. This amplification step performs several functions:
+
+- Prevents us from drawing current and allows to drive current to ADC and computer
+- Rejects common mode noise
+- Increases the range of the signal to fit the dynamic range of our digitizer
+
+.. youtube:: NP6nE5P82e8
+ :align: center
+ :width: 100%
\ No newline at end of file
diff --git a/courses/open-ephys/theory-day-3/index.rst b/courses/open-ephys/theory-day-3/index.rst
new file mode 100644
index 00000000..9458512c
--- /dev/null
+++ b/courses/open-ephys/theory-day-3/index.rst
@@ -0,0 +1,238 @@
+.. _theory-day-3:
+
+.. |Na+| replace:: Na\ :sup:`+`\
+.. |Cl-| replace:: Cl\ :sup:`-`\
+.. |Ca2+| replace:: Ca\ :sup:`2+`\
+.. |K+| replace:: K\ :sup:`+`\
+.. |Rs| replace:: R\ :sub:`s`\
+.. |Rm| replace:: R\ :sub:`m`\
+.. |Re| replace:: R\ :sub:`e`\
+.. |Rsh| replace:: R\ :sub:`sh`\
+.. |Ce| replace:: C\ :sub:`e`\
+.. |Csh| replace:: C\ :sub:`sh`\
+.. |Vin| replace:: V\ :sub:`in`\
+.. |Vec| replace:: V\ :sub:`ec`\
+.. |Vout| replace:: V\ :sub:`out`\
+.. |Ve| replace:: V\ :sub:`e`\
+.. |Za| replace:: Z\ :sub:`a`\
+.. |Ze| replace:: Z\ :sub:`e`\
+
+
+***********************************
+Theory Day 3
+***********************************
+
+.. contents:: Table of Contents
+ :depth: 2
+ :local:
+
+|
+
+An acquisition system must:
+
+* *Detect* changes in electric potential difference
+* Faithfully *transfer* this signal to our acquisition system output
+* **Distinguish interesting biological signals from other sources of electrical noise**
+
+Differential amplifiers remove common noise
+#########################################################
+
+Referencing
+**************************************
+
+We live in an (electrically) very noisy world. To get rid of some of this noise from our recording, we can use a reference point. This can be another electrode in the brain or a screw in the animal’s skull. The choice you make here is very important for your recording: the amplifier will output the difference between your recording electrode and your reference point. That means that the amplifier will do its best to get rid of any signal that the two share. If the recording electrode is picking up 50 Hz noise generated by the mains power supply in the walls, you want the amplifier to get rid of it, so it’s best to use a reference point that will also pick up this noise. However, if your reference is picking up signals that you are interested in, the amplifier will get rid of those too. To choose an appropriate reference, you have to decide what qualifies as noise in your experiment.
+
+Differential Amplifiers
+**************************************
+
+Talk
+***********************************
+
+.. raw:: html
+
+
+
+The amplification of the potential difference between the measuring electrode and the reference electrode (in the order of microvolts) is a crucial step. This is accomplished with differential amplifiers that amplify the difference and rejecting the 'common-mode' noise (i.e., noise identical in the recording and reference electrodes typically caused by motion artifacts and capacitive coupling of the body and electrode lead with power line fields (Nunez & Srinivasan, 2009)).
+
+Instrumentation amplifiers
+#########################################################
+
+Talk
+***********************************
+
+.. raw:: html
+
+
+
+
+
+Why do we need instrumentation amps?
+*************************************
+
+Why can't we just use 1 operational amplifier to get a nice signal?
+
+.. figure:: ../media/op_amp_spikes_ref.*
+ :align: center
+ :target: https://tinyurl.com/y4aps4r2
+
+
+To make this circuit differential, we need voltage dividers. But these are connecting our fragile signal to ground! Plus, any mismatch in the input impedances between ‘+’ and ‘-’ messes up the signal if there is a lot of common mode noise. In practical terms, there is always going to be a mismatch between these resistors, they simply cannot be produced in a way that makes them exactly equal.
+
+Why? Because this resistor is *also your electrode*. If you work with electrodes, have you measured their impedances? How similar are they? If you made these resistors as different as your electrodes are variable, this circuit will not work to eliminate common mode noise and amplify our spikes.
+
+The solution is to use *three* op-amps:
+
+.. figure:: ../media/three_op_amps.*
+ :align: center
+ :scale: 80
+
+|
+
+Here it is in the simulator:
+|
+
+.. figure:: ../media/instrumentation_amp_simulator.*
+ :align: center
+ :target: https://tinyurl.com/yjxekrv5
+ :alt: two operational amplifiers with negative feedback receive the measurement and reference electrode, respectively. Their outputs are fed into a third operation amplifier with negative feedback to form an instrumentation amplifier.
+
+Gain resistor
+-----------------------------------
+The voltages on either side of the gain resistor are fixed, because the op-amps are keeping them in place. If we have the same V and lower RGain = more current must travel through the resistor, and therefore more current through the feedback resistors of the two buffer op-amps. Those are fixed resistors: now we have a higher I for same R and therefore a higher voltage drop across these resistors. Both buffer op-amps now have to work harder to overcome this voltage drop and will output more extreme voltages. By decreasing the value of RGain, we are basically making the inputs to the final op-amp more different to each other, and therefore increasing the gain of the instrumentation amp.
+
+
+Common mode rejection ratio (CMRR)
+***********************************
+When the input impedances of the differential amplifier weren’t matched, part of the input signal that was common to both inputs, and thus should be cancelled out, actually appeared in the output. A common way to model how well an amplifier subtracts one input to the other is the following:
+We define each input (+ and -) to be a sum of an individual voltage (V1 or V2) plus a voltage common to both. In our arms, or the brain of an animal, this common voltage (Vc) could be electrical noise or muscle activity we are not interested in and want to discard. In this case, the inputs would be:
+
+.. math::
+ V+ = V1 + Vc
+.. math::
+ V- = V2 + Vc
+
+(In some examples of a differential amplifier, V2 is ground 0V, which is a perfectly valid value). In an **ideal** differential amplifier, the output should be the difference of both amplified by a factor:
+
+.. math::
+ Vout = Ad (V+ - V-)
+
+.. math::
+ = Ad ((V1+Vc)-(V2+Vc))
+
+.. math::
+ = Ad (V1-V2)
+
+Where Ad is the differential gain, the factor by which the differential signal is amplified.
+Here, the unwanted, common signals cancel out and only the signal we are interested in is amplified.
+
+A **real** amplifier, however, acts in a different way. As we’ve seen, small imperfections can lead to part of the common voltages being amplified as well. In this case, the output of a real amplifier ends up being:
+
+.. math::
+
+ Vout = Ad (V1 - V2 ) + Ac * Vc
+
+In addition to the differential gain, a new term 'Ac', or common gain, appears. This amplifies the signal common to both inputs. Of course, we want an amplifier to have a differential gain as high as possible and a common gain as low as possible (ideally, Ac would be 0). The relation between these two gains tells us how good an amplifier is at amplifying only the differential signals. This is called the Common Mode Rejection Ratio, or CMRR, simply defined as
+
+.. math::
+ CMRR = \frac{Ad}{Ac}
+
+or
+
+.. math::
+ CMRR = 20log\frac{Ad}{Ac}
+
+if measured in decibels.
+
+The higher the CMRR, the better the amplifier is at cancelling out the signals common to both inputs.
+Instrumentation amplifiers are not completely immune to common input noise. They are real circuits and, as such, there are multiple ways for these common signals to bleed out into the output. They have, however, a very high CMRR. Comparing the two devices we’ve been using, the operational amplifier LM358 has a CMRR of 80dB while the instrumentation amplifier has a CMRR of 120dB, 100 times higher! (Sounds underwhelming? Remember decibels are logarithmic; the difference between 80 and 120 dB in terms of sound is the difference between a toilet flushing and a jet engine).
+
+
+.. _refgroundref:
+
+Why do we need a ground electrode?
+###################################
+
+When we build our EMG circuit, we will use three electrodes: measurement (+), reference (-), and ground. Why do we have a ground electrode (or ground pin or screw) when we already have ‘+’ and ‘-’ inputs? This is a bit tricky, and there's multiple ways to understand it.
+
+.. raw:: html
+
+
+
+
+
+
+Imagine you just walked across a carpet and you're charged to 10kV. Now you want to do a differential measurement of EMG (or EEG). In theory, as far as we've really talked about until now, this should work via the magic of common-mode rejection. However, remember the circuit that is inside the instrumentation amp:
+
+
+.. figure:: ../media/instrumentation_amp_simulator.*
+ :align: center
+ :target: https://tinyurl.com/yjxekrv5
+
+
+The ‘-’ inputs of the two input op-amps are connected to ground, via a bunch of resistors. If you are charged to 10kV compared to Ground, we’re asking these op-amps to deal with very high differences in voltage, and they will saturate. Even if here we did not include rails in the simulation, remember that each op-amp can only go as high or low as its voltage rails (3V in our case, so with a 100x gain, a 0.03V input saturates the amplifier).
+
+|
+
+Remember the common mode rejection ratio. If our amplifier is good at rejecting 99.99% of the common mode, but 0.01% makes it through, in the range of volts, this could still be enough to prevent us from resolving microvolt spikes.
+
+|
+
+Attaching a ground electrode to ourselves, and then connecting this to the ground of our acquisition system, brings our body to 0V from the perspective of the acquisition system. The remaining noise fluctuations are still there, but the voltage difference is not as big anymore. We will still have residual 50 or 60Hz noise from the mains supply, plus other muscles, electrostatic charge, bodies moving through the fields in the room and so on, but these can all be handled by the amplifier.
+
+|
+
+The last, related, issue is that the output of the whole thing is relative to ground. At some point you want to connect this to a PC, which sits at ground level.
+
+|
+
+Practically, all this means that we want to ground our subjects as well as possible. For tetrode recordings in mice, we use a large ‘ground screw’ with low impedance to ground, so that we can effectively discharge the mouse.
+
+|
+
+One more detail: Ground is not (always) earth, in many cases it is just a certain circuit we treat as 0 that can provide or sink a lot of current. That circuit can have noise on it, just like any other circuit. If the ground has a lot of 50/60Hz noise, we’ll be charging and discharging the animal (any animal is also a capacitor) constantly through the ground connection. If the ground screw/electrode is low enough impedance and close to our recording site, we’ll manage to keep the animal’s voltage equal to the changing GND level and we won't notice this noise. However, if we put the ground screw/electrode too far away from where we record, e.g. we put the ground connection on the tail (extreme example), then the head of the animal won’t be sufficiently charged/discharged and we’ll encounter what will look like 50/60Hz noise in our tetrode recordings.
+
+.. _reffilter:
+
+Low and High pass filtering
+###################################
+
+Filters are used to remove certain frequencies from our data. We can do this in hardware or in software. Usually hardware filtering (implemented in the amplifier circuit) is used to increase (apparent) signal to noise ratio by rejecting unwanted frequencies and to prevent signal aliasing (e.g., bandpass between 0.5 and 2 kHz).
+Remember the exercise where we measured the voltage across our fingers with the oscilloscope, and saw very high values. Even with a differential amplifier, we usually have a decent amount of slow (~<10Hz or so) voltages that are simply too big for the amplifier or ADC (analog to digital converter). Any voltages above or below the amplifier rails (or above/below the input range of the digitizer) will be ‘clipped’ and all we’ll see is a constant value.
+The solution is to remove the large amplitude slow components, so we can fit the lower amplitude, faster, interesting components into our dynamic range.
+
+.. figure:: ../media/ADC_saturation.*
+ :align: center
+ :alt: The analog to digital converter cannot detect signals that cross over its +3 high rail. If the true signal is more than +3 V, this will still be represented as +3, resulting in a flat line for all values over +3, however high they may truly be.
+
+Therefore, high-pass filters first remove the large DC offsets present at the electrode-extracellular interface, along with any undesired low-frequency signals (e.g., movement artefacts). Additionally, low-pass filters must be configured to less than half of the ADC frequency sampling rate (Nyquist limit) to prevent aliasing, and may also be used to block undesired high-frequency signals and artefacts. For instance, if our sampling frequency is 30 kHz, the low pass filter should be ~15 kHz. Below is an example of the Intan headstage circuit.
+
+.. figure:: ../media/inside_intan.*
+ :align: center
+ :alt: The intan chip used in many headstages contains high pass analog filters and a differential amplifier for each ephys channel.
+
+Low-pass filters
+***********************************
+
+These filters block high frequencies. This is basically another voltage divider, with a frequency-dependent component. You’ve already seen one of these when you charged/discharged a capacitor! The exponential decay of the capacitor gets convolved with our signal. Remember that the impedance of our capacitor decreases as the signal frequency increases. At low frequencies, the high impedance of the capacitor means we get a large voltage drop over the capacitor, and more of our input signal can reach our Vout.
+
+.. figure:: ../media/low_pass.*
+ :align: center
+ :scale: 60
+ :target: https://www.falstad.com/circuit/e-filt-lopass.html
+ :alt: a resistor with capacitor to ground forms a low-pass filter
+
+
+High-pass filters
+***********************************
+
+This is the same `idea. `_
+With increasing signal frequency, the impedance of the capacitor decreases (day 1), reducing the voltage drop over the capacitor and sending more signal to the output.
+
+.. figure:: ../media/high_pass.*
+ :align: center
+ :scale: 70
+ :target: https://www.falstad.com/circuit/e-filt-hipass.html
+ :alt: a capacitor with resistor to ground forms a low-pass filter
+
+
+These are called `RC filters` because they’re built from a resistor (R) and a capacitor (C). Because there's only one of each, we call them ‘single pole’. In real life, filters are built from more than one pair in order to get specific characteristics. This goes beyond the scope of this course but there are entire classes on this topic.
\ No newline at end of file
diff --git a/courses/open-ephys/theory-day-4/index.rst b/courses/open-ephys/theory-day-4/index.rst
new file mode 100644
index 00000000..089b02bd
--- /dev/null
+++ b/courses/open-ephys/theory-day-4/index.rst
@@ -0,0 +1,64 @@
+.. _theory-day-4:
+
+***********************************
+Theory Day 4
+***********************************
+
+.. |Na+| replace:: Na\ :sup:`+`\
+.. |Cl-| replace:: Cl\ :sup:`-`\
+.. |Ca2+| replace:: Ca\ :sup:`2+`\
+.. |K+| replace:: K\ :sup:`+`\
+.. |Rs| replace:: R\ :sub:`s`\
+.. |Rm| replace:: R\ :sub:`m`\
+.. |Re| replace:: R\ :sub:`e`\
+.. |Rsh| replace:: R\ :sub:`sh`\
+.. |Ce| replace:: C\ :sub:`e`\
+.. |Csh| replace:: C\ :sub:`sh`\
+.. |Vin| replace:: V\ :sub:`in`\
+.. |Vec| replace:: V\ :sub:`ec`\
+.. |Vout| replace:: V\ :sub:`out`\
+.. |Ve| replace:: V\ :sub:`e`\
+.. |Za| replace:: Z\ :sub:`a`\
+.. |Ze| replace:: Z\ :sub:`e`\
+
+.. contents:: Table of Contents
+ :depth: 2
+ :local:
+
+.. _refdigitization:
+
+Digitization
+###################################
+The purpose of digitization is to convert amplified signals into digital values. Why do we digitize neural signals? To protect them from noise, and so that we can process and store them.
+First, the output of the amplifier (Vout) should match the digitizer dynamic range. Your analog signal should ‘occupy’ as much as possible, i.e. all discrete values in the digitization range. In other words, digitization range should match maximum analog signal. If the dynamic range is too small the signal will saturate, and if it is too large it will decrease effective signal resolution.
+
+.. figure:: ../media/3bitADC.*
+ :align: center
+
+If you have a voltage divider and an open-loop op-amp (comparator) you can already build a circuit that checks if your analog signal is above or below a certain value. Now instead of one voltage divider, you could have a whole ‘ladder’, creating intermediate values, and compare to these. This is an incredibly inefficient way to make an ADC.
+
+Here’s what this may look like:
+
+.. figure:: ../media/comparator_ladder.*
+ :align: center
+ :target: https://tinyurl.com/yadu834g
+
+In practice, many ADCs still use the same basic idea of using op-amps as comparators, but instead of comparing millions of values to obtain a precise measurement, they generate a reference voltage from an internal DAC and adjust that until it matches the input voltage, or use some other clever tricks.
+
+.. figure:: ../media/2vs3bitresolution.*
+ :align: center
+
+Typically AD converters have 12 to 16 bit resolution (4096 to 65536 discrete values) for neural signals, which is usually enough because of the size of the signals we want (spikes etc), and because the thermal noise floor of typical electrodes is similar to the achievable resolution anyway: better digitizers would just measure more of that noise. If you want to read more about that, have a look `here. `_
+
+Talk: Acquisition and Synchronization
+########################################
+One of the most common pitfalls in Neuroscience is correctly synchronizing multiple datastreams. How do you know whether your imaging and electrophysiology are aligned in time? How many different clocks do you have on your set up, and which of those can you trust?
+
+.. raw:: html
+
+
+
+
+
+
+The code for the exercises Filipe shows is available `on google drive `_ if you want to try it out yourself.
\ No newline at end of file
diff --git a/guides/usage-guides/skin-preparation/index.rst b/guides/usage-guides/skin-preparation/index.rst
index 5e3b91fb..c56152ef 100644
--- a/guides/usage-guides/skin-preparation/index.rst
+++ b/guides/usage-guides/skin-preparation/index.rst
@@ -8,12 +8,12 @@ Why skin preparation is important?
Proper skin preparation is crucial before recording any biopotential signal be it Electrocardiography (ECG), Electromyography (EMG), Electroencephalography (EEG), or Electrooculography (EOG).
-- ``Clean skin surface`` Removes dead skin cells, oils, & other substances that increases skin impedance.
-- ``Improve impedance`` Improves the conduction of electrical signals from the body to the recording equipment and minimizes impedance.
-- ``Electrode-skin contact`` Ensures optimal contact between the electrodes and the skin surface.
-- ``Signal quality`` Enhances the overall quality of recorded signals, providing clear & reliable data for analysis & improves the ability to capture subtle variations in biopotential signals.
-- ``Consistency in recordings`` Reduces variability in signal quality, making it easier to make any Human-Computer Interface (HCI), Brain-Computer Interface (BCI) project or a real-world application.
-- ``Long term adhesion`` Facilitates long-term adhesion & stable placement of electrodes to the skin during extended signal monitoring.
+- ``Clean skin surface:`` Removes dead skin cells, oils, & other substances that increases skin impedance.
+- ``Improve impedance:`` Improves the conduction of electrical signals from the body to the recording equipment and minimizes impedance.
+- ``Electrode-skin contact:`` Ensures optimal contact between the electrodes and the skin surface.
+- ``Signal quality:`` Enhances the overall quality of recorded signals, providing clear & reliable data for analysis & improves the ability to capture subtle variations in biopotential signals.
+- ``Consistency in recordings:`` Reduces variability in signal quality, making it easier to make any Human-Computer Interface (HCI), Brain-Computer Interface (BCI) project or a real-world application.
+- ``Long term adhesion:`` Facilitates long-term adhesion & stable placement of electrodes to the skin during extended signal monitoring.
Kit Contents
**************
@@ -96,7 +96,9 @@ Wipe away excess gel with alcohol swabs or wet wipes.
Wipe away access gel
-.. warning:: Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation.
+.. warning:: - Using alcohol swabs can dry out the skin, so don't use them if your skin is already dry.
+
+ - Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation.
Step 5: Measuring the signals
=================================
diff --git a/guides/usage-guides/using-bioamp-bands/index.rst b/guides/usage-guides/using-bioamp-bands/index.rst
index b41dd115..d52e3996 100644
--- a/guides/usage-guides/using-bioamp-bands/index.rst
+++ b/guides/usage-guides/using-bioamp-bands/index.rst
@@ -13,15 +13,15 @@ Why use BioAmp Bands?
Usually, people use gel electrodes to record biopotential signals from the skin surface. But, it has its own disadvantages. So we came up with these BioAmp Bands using which users can enjoy a more comfortable, cost-effective, and hassle-free experience while recording biopotential signals.
-- :bdg-primary:`Comfort` BioAmp Bands are generally more comfortable to wear than gel electrodes, especially for long-term recordings. They conform to the body's shape and avoid the sticky, sometimes irritating sensation of gel electrodes.
+- :bdg-primary:`Comfort:` BioAmp Bands are generally more comfortable to wear than gel electrodes, especially for long-term recordings. They conform to the body's shape and avoid the sticky, sometimes irritating sensation of gel electrodes.
-- :bdg-secondary:`Reusability` Unlike gel electrodes, which are often single-use and need to be replaced frequently, BioAmp Bands can be reused multiple times. This makes them more cost-effective and environmentally friendly.
+- :bdg-secondary:`Reusability:` Unlike gel electrodes, which are often single-use and need to be replaced frequently, BioAmp Bands can be reused multiple times. This makes them more cost-effective and environmentally friendly.
-- :bdg-success:`Ease of Use` These bands are easy to wear and adjust, reducing the hassle of setup and ensuring consistent placement.
+- :bdg-success:`Ease of Use:` These bands are easy to wear and adjust, reducing the hassle of setup and ensuring consistent placement.
-- :bdg-info:`Hygiene` They can be easily cleaned and sanitized between uses, reducing the risk of skin irritation and infections. Gel electrodes, on the other hand, can leave residue on the skin surface.
+- :bdg-info:`Hygiene:` They can be easily cleaned and sanitized between uses, reducing the risk of skin irritation and infections. Gel electrodes, on the other hand, can leave residue on the skin surface.
-- :bdg-danger:`Performance` The bands can provide stable and reliable signal recordings depending on your environment conditions. For hot/humid conditions, the bands usually perform better while recording the signals. But if the weather is cold causing dry skin, then it is recommended to prepare the skin properly and apply electrode gel between the metallic part of cable and skin surface. If you feel that the skin impedence is increasing, then reapply electrode gel frequently. The other option is to use gel electrodes after preparing the skin properly.
+- :bdg-danger:`Performance:` The bands can provide stable and reliable signal recordings depending on your environment conditions. For hot/humid conditions, the bands usually perform better while recording the signals. But if the weather is cold causing dry skin, then it is recommended to prepare the skin properly and apply electrode gel between the metallic part of cable and skin surface. If you feel that the skin impedence is increasing, then reapply electrode gel frequently. The other option is to use gel electrodes after preparing the skin properly.
Types of BioAmp Bands
@@ -29,7 +29,7 @@ Types of BioAmp Bands
There are 3 types of BioAmp Bands and all these bands offer targeted and efficient solutions for recording biopotential signals from the muscles, heart, and brain, making them versatile tools for a wide range of HCI/BCI applications.
-1) Muscle BioAmp Band
+1. Muscle BioAmp Band
==========================
Muscle BioAmp Band (EMG Band) is a stretchable band that can be connected to any of our Muscle BioAmp Hardware or any EXG sensor using a BioAmp Cable. It allows you to record your muscle signals hassle-free.
@@ -55,7 +55,7 @@ Muscle BioAmp Band (EMG Band) is a stretchable band that can be connected to any
| Wearable | Yes |
+---------------------+--------------------------------------------+
-2) Heart BioAmp Band
+2. Heart BioAmp Band
==========================
Heart BioAmp Band (ECG Band) is a stretchable band that can be connected to any of our Heart BioAmp Hardware or any EXG sensor using BioAmp Cable. It allows you to record your ECG signals hassle-free.
@@ -81,7 +81,7 @@ Heart BioAmp Band (ECG Band) is a stretchable band that can be connected to any
| Wearable | Yes |
+---------------------+--------------------------------------------+
-3) Brain BioAmp Band
+3. Brain BioAmp Band
==========================
Brain BioAmp Band (EEG Band) is a stretchable band that can be connected to any of our Brain BioAmp Hardware or any EXG sensor using BioAmp Cable to record signals from the brain hassle-free.
@@ -130,45 +130,90 @@ Assembly
1. Take your Muscle BioAmp Band, hold the side of the band that has buckle on it and align the top part of the buckle with the flat surface of the snap.
-.. figure:: media/muscle-bioamp-band/emg-band-assembly-1.gif
- :align: center
+.. only:: html
-2. Take the other end of the band and insert it in the buckle.
+ .. figure:: media/muscle-bioamp-band/emg-band-assembly-1.*
+ :align: center
-.. figure:: media/muscle-bioamp-band/emg-band-assembly-2.gif
- :align: center
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-1.*
+ :align: center
+
+1. Take the other end of the band and insert it in the buckle.
+
+.. only:: html
+
+ .. figure:: media/muscle-bioamp-band/emg-band-assembly-2.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-2.*
+ :align: center
+
+ .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-3.*
+ :align: center
3. Your band is now ready to use. You can also adjust the size of the band according to your targeted muscle.
-.. figure:: media/muscle-bioamp-band/adjust-band-size.gif
- :align: center
+.. only:: html
+
+ .. figure:: media/muscle-bioamp-band/adjust-band-size.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/adjust-band-size.*
+ :align: center
Skin Preparation
===================
Apply Nuprep Skin Preparation Gel on the skin surface where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.
-For more information, please check out detailed step by step `skin preparation guide `_.
+For more information, please check out detailed step by step :ref:`skin-preparation`.
Measure EMG
=============
1. Flip the band and snap the dry electrodes of the BioAmp Cable on it as shown below.
-.. figure:: media/muscle-bioamp-band/connecting-cable.gif
- :align: center
+.. only:: html
-2. Flip the band again and wear it on your arm in such a way that IN+ and IN- are placed on the arm near the ulnar nerve and REF (reference) on the far side of the band.
+ .. figure:: media/muscle-bioamp-band/connecting-cable.*
+ :align: center
-.. figure:: media/muscle-bioamp-band/wearing-band.gif
- :align: center
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/connecting-cable.*
+ :align: center
+
+1. Flip the band again and wear it on your arm in such a way that IN+ and IN- are placed on the arm near the ulnar nerve and REF (reference) on the far side of the band.
+
+.. only:: html
+
+ .. figure:: media/muscle-bioamp-band/wearing-band.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/wearing-band.*
+ :align: center
.. note:: Make sure the dry electrodes (shiny parts of the BioAmp Cable) are in direct contact with the skin.
3. Now put a small amount of electrode gel or Ten20 paste between the skin and dry electrodes to get the best signal acquisition.
+
+.. only:: html
-.. figure:: media/muscle-bioamp-band/applying-gel.gif
- :align: center
+ .. figure:: media/muscle-bioamp-band/applying-gel.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/muscle-bioamp-band/images/applying-gel.*
+ :align: center
.. note:: - After using the band, don't leave the gel residue on the dry electrodes longer than an hour as it may corrode them over a period of time.
- Wash the band with liquid soap and rinse it properly after every use. Use it again only when it is completely dry.
@@ -181,20 +226,37 @@ Skin Preparation
Apply Nuprep Skin Preparation Gel on your chest where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.
-For more information, please check out detailed step by step `skin preparation guide `_.
+For more information, please check out detailed step by step :ref:`skin-preparation`.
Assembly
============
1. Take your Heart BioAmp Band and wrap the band around your chest in such a way that the pointy part of the snap touches your chest and the flat part is on the outer side.
-.. figure:: media/heart-bioamp-band/wearing-band.gif
- :align: center
+.. only:: html
+
+ .. figure:: media/heart-bioamp-band/wearing-band.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/heart-bioamp-band/images/wearing-band.*
+ :align: center
2. Now insert the loose end of the band into the buckle and tighten it by pulling the strap.
-.. figure:: media/heart-bioamp-band/band-assembly.gif
- :align: center
+.. only:: html
+
+ .. figure:: media/heart-bioamp-band/band-assembly.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/heart-bioamp-band/images/band-assembly.*
+ :align: center
+
+ .. figure:: media/heart-bioamp-band/images/band-assembly-2.*
+ :align: center
3. Your band is now ready to use. You can also adjust the size of the band according to your chest size.
@@ -203,15 +265,29 @@ Measure ECG
1. Snap the IN- cable on the left most side of the band, IN+ cable in the middle, and REF cable on the right side as shown below.
-.. figure:: media/heart-bioamp-band/connecting-cable.gif
- :align: center
+.. only:: html
+
+ .. figure:: media/heart-bioamp-band/connecting-cable.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/heart-bioamp-band/images/connecting-cable.*
+ :align: center
.. note:: Make sure the dry electrodes (shiny parts of the BioAmp Cable) are in direct contact with the skin.
2. Now put a small amount of electrode gel or Ten20 paste between the skin and dry electrodes to get the best signal acquisition.
-.. figure:: media/heart-bioamp-band/electrode-gel.gif
- :align: center
+.. only:: html
+
+ .. figure:: media/heart-bioamp-band/electrode-gel.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/heart-bioamp-band/images/electrode-gel.*
+ :align: center
.. note:: - After using the band, don't leave the gel residue on the dry electrodes longer than an hour as it may corrode them over a period of time.
- Wash the band with liquid soap and rinse it properly after every use. Use it again only when it is completely dry.
@@ -223,38 +299,38 @@ Assembly
===========
You get the band in two parts - the longer part consists of buckles at both ends and the shorter one has loose ends on both sides.
-1) Hold one end of the longer band and align the top part of the buckle with the flat surface of the snap.
+1. Hold one end of the longer band and align the top part of the buckle with the flat surface of the snap.
-2) Now take the shorter band and insert it into the buckle of longer band.
+2. Now take the shorter band and insert it into the buckle of longer band.
-3) Repeat step 1 and 2 for the other buckle on the longer band.
+3. Repeat step 1 and 2 for the other buckle on the longer band.
-4) Your band is now ready to use. You can also adjust the size of the band according to your head size.
+4. Your band is now ready to use. You can also adjust the size of the band according to your head size.
Skin Preparation
===================
Apply Nuprep Skin Preparation Gel on your targeted area (visual cortex or prefrontal cortex) where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.
-For more information, please check out detailed step by step `skin preparation guide `_.
+For more information, please check out detailed step by step :ref:`skin-preparation`.
Measure 1-channel EEG
========================
-1) Flip the band, take your BioAmp Cable, and snap the REF cable on a gel electrode. Now snap the IN- and IN+ cable on:
+1. Flip the band, take your BioAmp Cable, and snap the REF cable on a gel electrode. Now snap the IN- and IN+ cable on:
- Fp1 and Fp2 positions for recording EEG from prefrontal cortex
- O1 and O2 positions for recording EEG from visual cortex
.. note:: The electrode positions mentioned above are according to `International 10-20 sytem for recording EEG `_.
-2) Flip the band again and wear it in a way so that the dry electrodes (shiny parts of the cable) are in contact with:
+2. Flip the band again and wear it in a way so that the dry electrodes (shiny parts of the cable) are in contact with:
- skin surface on the forehead (if recording from prefrontal cortex)
- scalp surface on the back side of your head (if recording from visual cortex)
-3) Peel of the plastic backing of the gel electrode and place it on the bony part behind your earlobe.
+3. Peel of the plastic backing of the gel electrode and place it on the bony part behind your earlobe.
.. note:: While placing the gel electrodes on the skin, make sure to place the non-sticky tab of the electrode in the direction opposite to your hair growth. This allows you to remove the electrodes easily without pulling off much body hair.
-4) Now put a small amount of electrode gel or Ten20 paste between the skin/scalp and dry electrodes to get the best signal acquisition.
\ No newline at end of file
+4. Now put a small amount of electrode gel or Ten20 paste between the skin/scalp and dry electrodes to get the best signal acquisition.
\ No newline at end of file
diff --git a/guides/usage-guides/using-bioamp-bands/media/heart-bioamp-band/images/band-assembly-2.png b/guides/usage-guides/using-bioamp-bands/media/heart-bioamp-band/images/band-assembly-2.png
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new file mode 100644
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new file mode 100644
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diff --git a/guides/usage-guides/using-bioamp-bands/media/muscle-bioamp-band/images/wearing-band.png b/guides/usage-guides/using-bioamp-bands/media/muscle-bioamp-band/images/wearing-band.png
new file mode 100644
index 00000000..21bd4d6d
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diff --git a/guides/usage-guides/using-gel-electrodes/index.rst b/guides/usage-guides/using-gel-electrodes/index.rst
index cebee068..6a434f25 100644
--- a/guides/usage-guides/using-gel-electrodes/index.rst
+++ b/guides/usage-guides/using-gel-electrodes/index.rst
@@ -79,14 +79,14 @@ Using the electrodes
Determine the target area from where you want to record the biopotential signals.
-.. warning:: For people having sensitive skin, it is recommended to use either gel electrodes with hydrogel/standard adhesive or use `BioAmp Bands `_.
+.. warning:: For people having sensitive skin, it is recommended to use either gel electrodes with hydrogel/standard adhesive or :ref:`use BioAmp Bands `.
1. Skin Preparation
======================
Remove any excessive hair on the targeted area. Apply Nuprep skin preparation gel on the skin surface where electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.
-For more information, please check out detailed step by step `skin preparation guide `_.
+For more information, please check out detailed step by step :ref:`skin-preparation`.
.. note:: Always ensure that the prepared skin area is dry prior to applying the gel electrodes.
diff --git a/hardware/bioamp/bioamp-exg-pill/index.rst b/hardware/bioamp/bioamp-exg-pill/index.rst
index 38e20754..45e967cd 100644
--- a/hardware/bioamp/bioamp-exg-pill/index.rst
+++ b/hardware/bioamp/bioamp-exg-pill/index.rst
@@ -15,7 +15,7 @@ just a few. It also works with any dedicated ADC, like the Texas Instruments ADS
.. note:: It is recommended to use Arduino UNO R4 while recording biopotential signals since it has 14-bit ADC and can record the signals much accurately.
-.. image:: ../../../media/bioamp-exg-pill.*
+.. figure:: ../../../media/bioamp-exg-pill.*
:align: center
What makes it different?
@@ -75,11 +75,11 @@ Software requirements
- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches in your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
- Download Backyard Brains' `Spike Recorder `_ according to the operating system you are using (Windows, OSX, Linux).
-.. image:: ../../../kits/diy-neuroscience/basic/media/byb.*
+.. figure:: ../../../kits/diy-neuroscience/basic/media/byb.*
Using the Hardware
*********************
@@ -94,9 +94,13 @@ Insert the provided BioAmp cable's JST PH connector and header pins from top as
.. figure:: media/assembly-step1.*
:align: center
+ `Soldering the connector & header pins on BioAmp EXG Pill`
+
.. figure:: media/bioamp-exg-pill-soldered.*
:align: center
+ `After soldering, BioAmp EXG Pill should look like this`
+
Step 2 (optional): Configure for ECG/EMG
==========================================
@@ -129,6 +133,8 @@ For all the examples provided, we are using the A0 pin of Arduino UNO R3. Connec
.. figure:: media/connections-with-arduino.*
:align: center
+ `Connections with Arduino UNO R3`
+
.. warning:: Take precautions while connecting to power, if power pins are to be swapped, your BioAmp EXG Pill will be fried and it’ll become unusable (DIE).
Step 4: Connecting electrode cable
@@ -136,7 +142,10 @@ Step 4: Connecting electrode cable
Connect the BioAmp cable to BioAmp EXG Pill by inserting the cable end in the JST PH connector as shown in the graphic below.
-.. image:: media/connection-with-cable.*
+.. figure:: media/connection-with-cable.*
+ :align: center
+
+ `Connections with BioAmp Cable v3`
Step 5: Skin Preparation
===========================
@@ -171,18 +180,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or
2. Peel the plastic backing from electrodes
3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.
-.. image:: media/emg.*
+.. figure:: media/emg.*
- **Using Muscle BioAmp Band:**
1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.
+
2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -191,11 +203,11 @@ Uploading the code
Connect the Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
-Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu,
+Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
disconnect your board and reopen the menu. The entry that disappears should be the
right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize
@@ -203,14 +215,15 @@ the EMG signals.
After opening the serial plotter make sure to select the baud rate to 115200.
-.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
+.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
Visualizing the EMG signals
----------------------------
Now flex your arm to visualize the muscle signals in real time on your laptop.
-.. image:: media/EMGEnvelop.*
+.. figure:: media/EMGEnvelop.*
+ :align: center
Step 6: Measuring ElectroCardioGraphy (ECG)
=============================================
@@ -232,7 +245,8 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or
2. Peel the plastic backing from electrodes
3. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side as shown in the diagram.
-.. image:: media/ecg.*
+.. figure:: media/ecg.*
+ :align: center
- **Using Heart BioAmp Band:**
@@ -240,20 +254,22 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or
2. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side.
3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
-**Tutorial on how to use the band:**
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
-.. youtube:: fr5iORsVyUM
- :align: center
- :width: 100%
+ **Tutorial on how to use the band:**
+
+ .. youtube:: fr5iORsVyUM
+ :align: center
+ :width: 100%
Uploading the code
---------------------
Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:
-ECG Filter: https://github.com/upsidedownlabs/Heart-BioAmp-Arduino-Firmware/blob/main/2_ECGFilter/2_ECGFilter.ino
+:fab:`github;pst-color-primary` `ECG Filter `_
-Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu,
+Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
disconnect your board and reopen the menu. The entry that disappears should be the
right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize
@@ -261,12 +277,15 @@ the signals.
After opening the serial plotter make sure to select the baud rate to 115200.
-.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
+.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
Visualizing the ECG signals
-----------------------------
-.. image:: media/bioamp-Exg-Pill-ECG.*
+Sit back, relax and see your ECG signals in real time on your laptop.
+
+.. figure:: media/bioamp-Exg-Pill-ECG.*
+ :align: center
Step 7: Measuring Electrooculography (EOG)
================================================
@@ -287,7 +306,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move
- **Horizontal EOG recording:**
-.. image:: media/eog-horizontal.*
+.. figure:: media/eog-horizontal.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -295,7 +315,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move
- **Vertical EOG recording:**
-.. image:: media/eog-vertical.*
+.. figure:: media/eog-vertical.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -306,9 +327,9 @@ Uploading the code
Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EOG Filter: https://github.com/upsidedownlabs/Eye-BioAmp-Arduino-Firmware/blob/main/2_EOGFilter/2_EOGFilter.ino
+:fab:`github;pst-color-primary` `EOG Filter `_
-Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu,
+Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
disconnect your board and reopen the menu. The entry that disappears should be the
right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize
@@ -316,12 +337,15 @@ the signals.
After opening the serial plotter make sure to select the baud rate to 115200.
-.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
+.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
Visualizing the EOG signals
------------------------------
-.. image:: media/bioamp-exg-pill-eog.*
+Move your eyes up-down or left-right to see your EOG signals in real time on your laptop.
+
+.. figure:: media/bioamp-exg-pill-eog.*
+ :align: center
Step 8: Measuring Electroencephalography (EEG)
===================================================
@@ -335,7 +359,7 @@ Step 8: Measuring Electroencephalography (EEG)
For recording EEG from different parts of the brain, you have to place the electrodes according to the `International 10-20 system for recording EEG `_.
-.. image:: ../../../kits/diy-neuroscience/basic/media/10-20-system.*
+.. figure:: ../../../kits/diy-neuroscience/basic/media/10-20-system.*
:align: center
Electrodes placement
@@ -345,7 +369,8 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or
- **Using gel electrodes to record from prefrontal cortex part of brain:**
-.. image:: media/eeg.*
+.. figure:: media/eeg.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -357,27 +382,29 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or
2. In this case, the REF (reference) should be connected using gel electrode. So connect the reference of BioAmp cable to the gel electrode, peel the plastic backing and place it at the bony part, on the back side of your earlobe.
3. Now put a small drop of electrode gel on the dry electrodes (IN+ and IN-) between the skin and metallic part of BioAmp cable to get the best results.
-.. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
+ **Tutorial on how to use the band:**
-**Tutorial on how to use the band:**
+ .. youtube:: O6qp7teT-sM
+ :align: center
+ :width: 100%
-.. youtube:: O6qp7teT-sM
- :align: center
- :width: 100%
+.. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same.
Uploading the code
-----------------------
Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:
-`Spike recorder arduino code `_
+:fab:`github;pst-color-primary` `Spike recorder arduino code `_
-Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu,
+Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your development board is connected. To find out the right COM port, screen
disconnect your board and reopen the menu. The entry that disappears should be the
right COM port. Now upload the code.
-.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
+.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
Visualizing the EEG signals
-------------------------------
@@ -386,6 +413,9 @@ Open the Spike Recorder software. When the Spike Recorder starts, it will start
the first icon on the top left corner of the screen, select the COM port on which your Arduino UNO is connected and click on connect.
.. figure:: ../../../kits/diy-neuroscience/basic/media/spike-recorder-configurations.*
+ :align: center
+
+ `Spike Recorder settings`
Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should
set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between
@@ -393,7 +423,10 @@ these frequencies.
Now everything is configured and connected. So close the settings window and start recording EEG signals.
-.. image:: ../../../kits/diy-neuroscience/basic/media/bioamp-exg-pill-eeg.*
+.. figure:: ../../../kits/diy-neuroscience/basic/media/bioamp-exg-pill-eeg.*
+ :align: center
+
+ `EEG signals being visualised in Spike Recorder`
The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin.
@@ -458,25 +491,49 @@ Project ideas & tutorials
:margin: 4 4 0 0
:gutter: 2
- .. grid-item-card:: Detecting heart beats
+ .. grid-item-card:: Controlling video game using brainwaves (EEG)
:text-align: center
- :link: https://youtu.be/uB5R-vGJjJo
+ :link: https://www.instructables.com/Controlling-Video-Game-Using-Brainwaves-EEG/
- .. grid-item-card:: Measuring heart rate
+ .. grid-item-card:: Visualising electrical impulses from eyes (EOG)
+ :text-align: center
+ :link: https://www.instructables.com/Visualizing-Electrical-Impulses-of-Eyes-EOG-Using-/
+
+ .. grid-item-card:: Recording EEG from visual cortex
:text-align: center
- :link: https://youtu.be/PvWtCFNK3_s
+ :link: https://www.instructables.com/Recording-EEG-From-Visual-Cortex-of-Brain-Using-Bi/
+
+ .. grid-item-card:: Recording EEG from prefrontal cortex
+ :text-align: center
+ :link: https://www.instructables.com/Recording-EEG-From-Pre-Frontal-Cortex-of-Brain-Usi/
+
+ .. grid-item-card:: Eye blink detection
+ :text-align: center
+ :link: https://www.instructables.com/Eye-Blink-Detection-by-Recording-EOG-Using-BioAmp-/
.. grid-item-card:: Creating a drowsiness detector
:text-align: center
- :link: https://youtu.be/h4F41mp4mWk
+ :link: https://www.instructables.com/Drowsiness-Detector-by-Detecting-EOG-Signals-Using/
+
+ .. grid-item-card:: Record publication-grade ECG
+ :text-align: center
+ :link: https://www.instructables.com/Record-Publication-Grade-ECG-at-Your-Home-Using-Bi/
+
+ .. grid-item-card:: Measuring heart rate
+ :text-align: center
+ :link: https://www.instructables.com/Measuring-Heart-Rate-Using-BioAmp-EXG-Pill/
+
+ .. grid-item-card:: Detecting heart beats
+ :text-align: center
+ :link: https://www.instructables.com/Detecting-Heart-Beats-Using-BioAmp-EXG-Pill/
- .. grid-item-card:: Detecting eye blinks
+ .. grid-item-card:: Record publication-grade EMG
:text-align: center
- :link: https://youtu.be/PfEJVa3gv6E
+ :link: https://www.instructables.com/Recording-Publication-Grade-Muscle-Signals-Using-B/
- .. grid-item-card:: Record EEG from visual cortex part of brain
+ .. grid-item-card:: Detecting up and down movement of eyes
:text-align: center
- :link: https://youtu.be/XENPUkfxLec
+ :link: https://www.instructables.com/Tracking-UP-and-DOWN-Movements-of-Eyes-Using-EOG/
These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and
Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech.
@@ -487,11 +544,17 @@ Project ideas & tutorials
Below are some project ideas that you can try making at your home.
- 1. `Recording EEG from visual cortex `_
- 2. `Measuring heart rate `_
- 3. `Detecting heart beats `_
- 4. `Creating a drowsiness detector `_
- 5. `Detecting eye blinks `_
+ 1. `Controlling video game using brainwaves (EEG) `_
+ 2. `Visualising electrical impulses from eyes (EOG) `_
+ 3. `Recording EEG from visual cortex part of brain `_
+ 4. `Recording EEG from prefrontal cortex part of brain `_
+ 5. `Eye blink detection `_
+ 6. `Creating a drowsiness detector `_
+ 7. `Record publication-grade ECG `_
+ 8. `Measuring heart rate `_
+ 9. `Detecting heart beats `_
+ 10. `Record publication-grade EMG `_
+ 11. `Detecting up and down movement of eyes `_
These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and
Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech
diff --git a/hardware/bioamp/bioamp-v1.5/index.rst b/hardware/bioamp/bioamp-v1.5/index.rst
index 9eebafec..926e1f52 100644
--- a/hardware/bioamp/bioamp-v1.5/index.rst
+++ b/hardware/bioamp/bioamp-v1.5/index.rst
@@ -73,20 +73,20 @@ Images below shows a quick overview of the hardware design.
Contents of the kit
********************
-.. image:: media/kit-contents.*
+.. figure:: media/kit-contents.*
Software requirements
**********************
Before you start using the kit, download Backyard Brains' `Spike Recorder `_ or `Audacity `_ according to the operating system you are using (Windows, OSX, Linux).
-.. figure:: ../../../kits/diy-neuroscience/basic/media/byb.*
+.. .. figure:: ../../../kits/diy-neuroscience/basic/media/byb.*
- **Backyard Brains Spike Recorder**
+.. **Backyard Brains Spike Recorder**
-.. figure:: media/audacity.*
+.. .. figure:: media/audacity.*
- **Audacity (An easy-to-use, multi-track audio editor and recorder)**
+.. **Audacity (An easy-to-use, multi-track audio editor and recorder)**
Assembling the kit
********************
@@ -103,91 +103,91 @@ You can get your own BioAmp v1.5 bag of parts from our `online stores `.
Step 4: Connecting 9V battery
===============================
Connect any 9V battery to BioAmp v1.5 using the 9V snap cable. Now activate the board by flipping ON the power switch, and you'll notice an LED light up, showing that the board is ready to use.
-.. image:: media/9v-battery.*
+.. figure:: media/9v-battery.*
+ :align: center
Step 5: Listen to your muscle signals
======================================
@@ -254,7 +269,8 @@ Using speakers
2. Switch on the speaker and turn the volume to maximum.
3. Flex and listen to your muscles.
-.. image:: media/listening-emg-2.*
+.. figure:: media/listening-emg-2.*
+ :align: center
Using wired earphones/headphones
----------------------------------------------
@@ -263,7 +279,9 @@ Using wired earphones/headphones
2. Plug it in your ears.
3. Flex and listen to your muscles.
-.. image:: media/listening-emg-3.*
+.. figure:: media/listening-emg-3.*
+ :align: center
+ :width: 80%
Step 6: Visualize EMG signals on mobile phone
===================================================
@@ -277,7 +295,9 @@ Using Phone Recorder app
2. Flex your muscle to be able to record the muscle signals.
3. If you want to extract that data then it will be saved by default as a .wav file but you can convert it in any other format according to your project requirements.
-.. image:: media/emg-in-mobile-2.*
+.. figure:: media/emg-in-mobile-2.*
+ :align: center
+ :width: 80%
Using Backyard Brains' Spike Recorder mobile app
------------------------------------------------
@@ -286,15 +306,17 @@ Using Backyard Brains' Spike Recorder mobile app
2. Open the app, click the setting icon on the top right corner and set the recording type to EMG.
3. Apply the 50Hz or 60Hz notch filter depending on the country you are living in. For example if you are in India then the AC current oscillates at a frequency of 50Hz but it oscillates at 60Hz frequency in USA. This AC current acts as a noise in the signals so we have to remove it by applying this notch filter.
-.. image:: media/spike-recorder-mobile.*
- :width: 80%
+.. figure:: media/spike-recorder-mobile.*
+ :width: 60%
:align: center
4. Again click on the setting icon to close it and you are ready.
5. Flex your muscles to be able to visualize the muscle signals (EMG).
6. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements.
-.. image:: media/emg-in-mobile.*
+.. figure:: media/emg-in-mobile.*
+ :width: 80%
+ :align: center
Step 7: Visualize the EMG signals on laptop
============================================
@@ -308,13 +330,15 @@ Using Backyard Brains' Spike Recorder
2. Open the software, click the setting icon on the top right corner and set the low band pass filter to 72Hz and high band pass filter to 720Hz.
3. Apply the 50Hz or 60Hz notch filter depending on the country you are living in. For example if you are in India then the AC current oscillates at a frequency of 50Hz but it oscillates at 60Hz frequency in USA. This AC current acts as a noise in the signals so we have to remove it by applying this notch filter.
-.. image:: media/spike-recorder-laptop.*
+.. figure:: media/spike-recorder-laptop.*
+ :align: center
4. Again click on the setting icon to close it and you are ready.
5. Flex your muscles to be able to visualize the muscle signals (EMG)
6. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements.
-.. image:: media/emg-in-laptop.*
+.. figure:: media/emg-in-laptop.*
+ :align: center
Using Audacity
----------------
@@ -324,6 +348,7 @@ Using Audacity
3. Flex your muscles to be able to visualize the muscle signals (EMG)
4. By default the EMG data would be recorded as a .wav file but you can convert it in any other format as per your project requirements.
-.. image:: media/emg-in-audacity.*
+.. figure:: media/emg-in-audacity.*
+ :align: center
diff --git a/hardware/bioamp/bioamp-v1.5/media/spike-recorder-mobile.jpg b/hardware/bioamp/bioamp-v1.5/media/spike-recorder-mobile.jpg
index b6d5abd0..56627fd3 100644
Binary files a/hardware/bioamp/bioamp-v1.5/media/spike-recorder-mobile.jpg and b/hardware/bioamp/bioamp-v1.5/media/spike-recorder-mobile.jpg differ
diff --git a/hardware/bioamp/muscle-bioamp-biscute/index.rst b/hardware/bioamp/muscle-bioamp-biscute/index.rst
index ec737db2..f12c7e79 100644
--- a/hardware/bioamp/muscle-bioamp-biscute/index.rst
+++ b/hardware/bioamp/muscle-bioamp-biscute/index.rst
@@ -1,4 +1,4 @@
-.. _muscle_bioamp-biscute:
+.. _muscle-bioamp-biscute:
Muscle BioAmp Biscute
######################
@@ -44,52 +44,67 @@ Hardware
**********
Images below shows a quick overview of the hardware design.
-.. grid:: 1 1 2 2
- :margin: 4 4 0 0
- :gutter: 2
+.. only:: html
- .. grid-item::
-
- .. card::
+ .. grid:: 1 1 2 2
+ :margin: 4 4 0 0
+ :gutter: 2
- **PCB Front**
- ^^^^^
- .. figure:: media/front.*
+ .. grid-item::
+
+ .. card::
+
+ PCB Front
+ ^^^^^
+ .. figure:: media/front.*
+
+ .. grid-item::
+
+ .. card::
- .. grid-item::
-
- .. card::
+ PCB Back
+ ^^^^^
+ .. figure:: media/back.*
- **PCB Back**
- ^^^^^
- .. figure:: media/back.*
+.. only:: latex
+
+ .. figure:: media/front.*
+ :width: 50%
+
+ .. figure:: media/back.*
+ :width: 50%
.. figure:: media/assembled.*
:align: center
+ :width: 50%
- **Assembled PCB**
+ Assembled PCB
.. figure:: media/dimensions.*
:align: center
+ :width: 100%
- **PCB Layout**
+ PCB Layout
.. figure:: media/schematic.*
:align: center
+ :width: 90%
- **Schematic Diagram**
+ Schematic Diagram
Contents of the kit
********************
-.. image:: media/kit-contents.*
+.. figure:: media/kit-contents.*
+ :align: center
+ :width: 60%
Software requirements
**********************
- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
Assembling the kit
********************
@@ -98,100 +113,172 @@ You can get Muscle BioAmp BisCute from our `online stores ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -261,9 +353,9 @@ Uploading the code
Connect your Arduino UNO to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
@@ -280,9 +372,9 @@ Visualizing the EMG signals
Now flex your arm to visualize the muscle signals in real time on your laptop.
-.. image:: media/using-biscute.*
+.. figure:: media/using-biscute.*
+ :align: center
-
**Video tutorial:**
.. youtube:: ujFsAE0E0nk
diff --git a/hardware/bioamp/muscle-bioamp-blip/index.rst b/hardware/bioamp/muscle-bioamp-blip/index.rst
index 90ac4c00..3bc804a5 100644
--- a/hardware/bioamp/muscle-bioamp-blip/index.rst
+++ b/hardware/bioamp/muscle-bioamp-blip/index.rst
@@ -46,43 +46,66 @@ Hardware
Images below shows a quick overview of the hardware design.
-.. grid:: 1 1 2 2
- :margin: 4 4 0 0
- :gutter: 2
+.. .. only:: html
- .. grid-item::
+.. .. grid:: 1 1 2 2
+.. :margin: 4 4 0 0
+.. :gutter: 2
- .. card::
+.. .. grid-item::
- **PCB Front**
- ^^^^^
- .. figure:: media/muscle-bioamp-blip-front.*
+.. .. card::
- .. grid-item::
-
- .. card::
+.. **PCB Front**
+.. ^^^^^
+.. .. figure:: media/muscle-bioamp-blip-front.*
- **PCB Back**
- ^^^^^
- .. figure:: media/muscle-bioamp-blip-front.*
+.. .. grid-item::
+
+.. .. card::
+
+.. **PCB Back**
+.. ^^^^^
+.. .. figure:: media/muscle-bioamp-blip-front.*
+
+.. .. only:: latex
+
+.. .. figure:: media/muscle-bioamp-blip-front.*
+.. :align: center
.. figure:: media/muscle-bioamp-blip-assembled.*
:align: center
- :width: 400
+ :width: 60%
Assembled PCB
Contents of the kit
********************
-.. image:: media/blip-kit-contents.*
++---------------------+-----+
+| Contents of the kit | Qty |
++=====================+=====+
+| Muscle BioAmp Blip | 1 |
++---------------------+-----+
+| BioAmp Cable v3 | 1 |
++---------------------+-----+
+| Muscle BioAmp Band | 1 |
++---------------------+-----+
+| Boxy gel electrodes | 6 |
++---------------------+-----+
+
+.. figure:: media/blip-kit-contents.*
+ :align: center
+ :width: 80%
Software requirements
**********************
-- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
+Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+ :align: center
+ :width: 80%
Using the kit
****************
@@ -92,7 +115,9 @@ Step 1: Soldering connector & header pins
Solder the header pins and JST Ph 2.0mm connector on the Muscle BioAmp Blip as shown below. If you ordered assembled kit then you can skip this step and directly move to step 2.
-.. image:: media/soldering-blip.*
+.. figure:: media/soldering-blip.*
+ :width: 80%
+ :align: center
Step 2: Connections with the sensor
========================================
@@ -104,28 +129,35 @@ Directly connecting jumper cables
You can directly connect the male to female jumper cables on the header pins of Muscle BioAmp Blip at ``5V``, ``GND``, ``AN``.
-.. image:: media/blip-with-jumper-cables.*
+.. figure:: media/blip-with-jumper-cables.*
+ :width: 80%
+ :align: center
Connecting on breadboard
---------------------------
If you are thinking to connect more components/sensors and want to integrate Muscle BioAmp Blip in the complete circuit then it will be better to use a breadboard. Snap the Muscle BioAmp Blip on the breadboard and connect the jumper cables (male to male) at ``5V``, ``GND``, ``AN``.
-.. image:: media/blip-with-breadboard.*
+.. figure:: media/blip-with-breadboard.*
+ :width: 80%
+ :align: center
Connecting via mikroBUS port
-----------------------------
You can also connect the Muscle BioAmp Blip to any hardware that has mikroBUS™ port like mikroBUS™ shuttle, mikroBUS™ Arduino UNO Click Shield to name a few.
-.. image:: media/blip-with-shuttle.*
+.. figure:: media/blip-with-shuttle.*
+ :width: 80%
+ :align: center
Step 3: Connecting with Arduino UNO R3
=======================================
Connect ``5V`` of the sensor to ``5V`` of your Arduino UNO, ``GND`` to ``GND``, and ``AN`` to ``Analog pin A0`` via other end of the jumper cables. If you are connecting ``AN`` to any other analog pin, then you will have to change the `INPUT PIN` in the example arduino sketch accordingly.
-.. image:: media/blip-arduino-connections.*
+.. figure:: media/blip-arduino-connections.*
+ :align: center
.. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice.
@@ -134,7 +166,8 @@ Step 4: Connecting electrode cable
Connect the BioAmp cable to Muscle BioAmp Blip by inserting the cable end in the JST PH connector as shown.
-.. image:: media/blip-bioamp-cable.*
+.. figure:: media/blip-bioamp-cable.*
+ :align: center
Step 5: Skin Preparation
===============================================
@@ -155,13 +188,20 @@ Using gel electrodes
2. Peel the plastic backing from electrodes
3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.
-.. figure:: media/emg-connections-1.*
+.. only:: latex
+
+ .. figure:: media/emg-connections-1.*
+ :align: center
+ :width: 60%
- Muscle BioAmp Blip with breadboard
+ Muscle BioAmp Blip with breadboard
-.. figure:: media/emg-connections-2.*
+.. only:: html
- Muscle BioAmp Blip directly connected via jumper cables
+ .. figure:: media/emg-connections-1.*
+ :align: center
+
+ Muscle BioAmp Blip with breadboard
Using Muscle BioAmp Band
---------------------------
@@ -169,11 +209,12 @@ Using Muscle BioAmp Band
1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.
2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -182,9 +223,9 @@ Step 7: Uploading the code
Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
@@ -201,7 +242,8 @@ Step 8: Visualizing the EMG signals
Now flex your arm to visualize the muscle signals in real time on your laptop.
-.. image:: media/emg-recording.*
+.. figure:: media/emg-recording.*
+ :align: center
.. rubric:: Footnotes
diff --git a/hardware/bioamp/muscle-bioamp-blip/media/blip-kit-contents-2.png b/hardware/bioamp/muscle-bioamp-blip/media/blip-kit-contents-2.png
new file mode 100644
index 00000000..23535272
Binary files /dev/null and b/hardware/bioamp/muscle-bioamp-blip/media/blip-kit-contents-2.png differ
diff --git a/hardware/bioamp/muscle-bioamp-blip/media/blip-with-breadboard.png b/hardware/bioamp/muscle-bioamp-blip/media/blip-with-breadboard.png
old mode 100755
new mode 100644
index fe267973..e46dbc8a
Binary files a/hardware/bioamp/muscle-bioamp-blip/media/blip-with-breadboard.png and b/hardware/bioamp/muscle-bioamp-blip/media/blip-with-breadboard.png differ
diff --git a/hardware/bioamp/muscle-bioamp-blip/media/blip-with-jumper-cables.png b/hardware/bioamp/muscle-bioamp-blip/media/blip-with-jumper-cables.png
old mode 100755
new mode 100644
index 23f6f76b..96dd7aa2
Binary files a/hardware/bioamp/muscle-bioamp-blip/media/blip-with-jumper-cables.png and b/hardware/bioamp/muscle-bioamp-blip/media/blip-with-jumper-cables.png differ
diff --git a/hardware/bioamp/muscle-bioamp-candy/index.rst b/hardware/bioamp/muscle-bioamp-candy/index.rst
index dc04086d..ef51dc69 100644
--- a/hardware/bioamp/muscle-bioamp-candy/index.rst
+++ b/hardware/bioamp/muscle-bioamp-candy/index.rst
@@ -7,7 +7,7 @@ Overview
*********
A candy-size single-channel ElectroMyography (EMG) sensor for recording of muscle signals
-at an affordable cost. It is an SMD version of :ref:`muscle_bioamp-biscute` that can be used to make
+at an affordable cost. It is an SMD version of :ref:`muscle-bioamp-biscute` that can be used to make
amazing Human-Computer Interface (HCI) projects.
.. figure:: media/Muscle-BioAmp-Candy-front.*
@@ -45,33 +45,49 @@ Hardware
Images below shows a quick overview of the hardware design.
-.. grid:: 1 1 2 2
- :margin: 4 4 0 0
- :gutter: 2
+.. only:: html
- .. grid-item::
-
- .. card::
+ .. grid:: 1 1 2 2
+ :margin: 4 4 0 0
+ :gutter: 2
- **PCB Front**
- ^^^^^
- .. figure:: media/PCBfront.*
+ .. grid-item::
+
+ .. card::
- .. grid-item::
-
- .. card::
+ **PCB Front**
+ ^^^^^
+ .. figure:: media/PCBfront.*
- **PCB Back**
- ^^^^^
- .. figure:: media/PCBback.*
+ .. grid-item::
+
+ .. card::
+
+ **PCB Back**
+ ^^^^^
+ .. figure:: media/PCBback.*
+
+.. only:: latex
+
+ .. figure:: media/PCBfront.*
+ :width: 60%
+
+ PCB Front
+
+ .. figure:: media/PCBback.*
+ :width: 60%
+
+ PCB Back
.. figure:: media/muscle-bioamp-candy-front.*
:align: center
+ :width: 60%
Assembled PCB - Front
.. figure:: media/muscle-bioamp-candy-back.*
:align: center
+ :width: 60%
Assembled PCB - Back
@@ -88,14 +104,34 @@ Images below shows a quick overview of the hardware design.
Contents of the kit
********************
-.. image:: media/kit-contents.*
++--------------------------+-----+
+| Contents of the kit | Qty |
++==========================+=====+
+| Muscle BioAmp Candy | 1 |
++--------------------------+-----+
+| BioAmp Cable v3 | 1 |
++--------------------------+-----+
+| Jumper cables (set of 3) | 1 |
++--------------------------+-----+
+| Muscle BioAmp Band | 1 |
++--------------------------+-----+
+| Boxy gel electrodes | 3 |
++--------------------------+-----+
+
+.. figure:: media/kit-contents.*
+ :align: center
+
+ Kit contents
Software requirements
**********************
-- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
+Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+ :align: center
+
+ Arduino IDE v1.8.19
Using the kit
****************
@@ -103,10 +139,12 @@ Using the kit
Step 1: Connect Arduino UNO R3
=================================
-.. image:: media/arduino-candy-connection.*
-
Connect ``VCC`` to either ``5V`` or ``3.3V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Arduino UNO via jumper cables provided by us. If you are connecting ``OUT`` to any other analog pin, then you will have to change the `INPUT PIN` in the example arduino sketch accordingly.
+.. figure:: media/arduino-candy-connection.*
+ :align: center
+ :width: 70%
+
.. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice.
.. warning:: Take precautions while connecting to power, if power pins (GND & VCC) are to be swapped, your sensor will be fried and it’ll become unusable (DIE).
@@ -114,9 +152,11 @@ Connect ``VCC`` to either ``5V`` or ``3.3V``, ``GND`` to ``GND``, and ``OUT`` to
Step 2: Connecting electrode cable
========================================
-.. image:: media/candy-cable-connection.*
+Connect the BioAmp cable to Muscle BioAmp Candy by inserting the cable end in the JST PH connector as shown.
-Connect the BioAmp cable to Muscle BioAmp Candy by inserting the cable end in the JST PH connector as shown above.
+.. figure:: media/candy-cable-connection.*
+ :width: 70%
+ :align: center
Step 3: Skin Preparation
===============================================
@@ -139,18 +179,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or
2. Peel the plastic backing from electrodes
3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.
-.. image:: media/candy-emg.*
+.. figure:: media/candy-emg.*
+ :align: center
- **Using Muscle BioAmp Band:**
1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.
2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -159,9 +202,9 @@ Uploading the code
Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
@@ -178,7 +221,8 @@ Visualizing the EMG signals
Now flex your arm to visualize the muscle signals in real time on your laptop.
-.. image:: media/using-candy.*
+.. figure:: media/using-candy.*
+ :align: center
**Video tutorial:**
diff --git a/hardware/bioamp/muscle-bioamp-patchy/index.rst b/hardware/bioamp/muscle-bioamp-patchy/index.rst
index 4d5247a7..c6513e67 100644
--- a/hardware/bioamp/muscle-bioamp-patchy/index.rst
+++ b/hardware/bioamp/muscle-bioamp-patchy/index.rst
@@ -14,6 +14,7 @@ powerful BioAmp sensing technology for precise muscle signal recording. This ena
based Human-Computer Interface (HCI) easily.
.. figure:: media/Patchy-All-Colors.*
+ :align: center
Features & Specifications
**************************
@@ -69,7 +70,8 @@ Images below shows a quick overview of the hardware design.
Contents of the kit
********************
-.. image:: media/kit-contents.*
+.. figure:: media/kit-contents.*
+ :align: center
We have made a complete unboxing video of the kit. Please find the link below:
@@ -82,7 +84,8 @@ Software requirements
Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+ :align: center
Using the kit
****************
@@ -92,14 +95,15 @@ Step 1: Connect reference cable
Connect the reference cable to the Muscle BioAmp Patchy as shown in the diagram.
-.. image:: media/ref-cable-connection.*
+.. figure:: media/ref-cable-connection.*
+ :align: center
Step 2: Connecting sensor to gel electrodes
================================================
Snap the Muscle BioAmp Patchy on the gel electrodes (Don't peel the plastic backing from the electrodes at this moment).
-.. image:: media/patchy-electrode-connection.*
+.. figure:: media/patchy-electrode-connection.*
:width: 80%
:align: center
@@ -115,7 +119,8 @@ Step 4: Electrode Placements
Now peel off the plastic backing from the gel electrodes and place the Muscle BioAmp Patchy on the targeted muscle and the reference on the bony part of your elbow as shown in the diagram.
-.. image:: media/patchy-on-hand.*
+.. figure:: media/patchy-on-hand.*
+ :align: center
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -124,7 +129,10 @@ Step 5: Connect Arduino UNO R3
Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Arduino UNO via jumper cables provided by us. If you are connecting ``OUT`` to any other analog pin, then you will have to change the INPUT PIN in the arduino sketch accordingly.
-.. image:: media/pathcy-arduino-connections.*
+.. figure:: media/pathcy-arduino-connections.*
+ :align: center
+
+ Connections with Arduino UNO R3
.. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice.
@@ -133,11 +141,12 @@ Step 6: Upload the code
Connect your Arduino UNO to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
-.. image:: media/setup.*
+.. figure:: media/setup.*
+ :align: center
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
@@ -154,7 +163,8 @@ Step 7: Visualizing the EMG signals
Now flex your arm to visualize the muscle signals in real-time on your laptop.
-.. image:: media/patchy-emg.*
+.. figure:: media/patchy-emg.*
+ :align: center
**Video tutorial:**
diff --git a/hardware/bioamp/muscle-bioamp-shield/index.rst b/hardware/bioamp/muscle-bioamp-shield/index.rst
index f101e335..908ebcb5 100644
--- a/hardware/bioamp/muscle-bioamp-shield/index.rst
+++ b/hardware/bioamp/muscle-bioamp-shield/index.rst
@@ -13,7 +13,8 @@ BackYard Brains (BYB) `Muscle Spiker shield `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop.
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png
-
-Assembling the Kit
-********************
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+ :align: center
-You can get your own Muscle BioAmp Shield bag of parts from our `online stores `_ (shipping worldwide)
-and for assembling your shield you can take a look at `this interactive BOM `_ or the step by step guide below.
+ Download Arduino IDE v1.8.19
-.. note:: Follow the highlighted yellow shapes to assemble your shield!
+.. only:: html
-.. grid:: 1 1 2 2
- :margin: 2 2 0 0
- :gutter: 2
+ Assembling the Kit
+ ********************
- .. grid-item::
-
- .. figure:: media/Assembly/01_Bare_Board.*
+ You can get your own Muscle BioAmp Shield bag of parts from our `online stores `_ (shipping worldwide)
+ and for assembling your shield you can take a look at `this interactive BOM `_ or the step by step guide below.
- **Step 1 - Bare Board**
+ .. note:: Follow the highlighted yellow shapes to assemble your shield!
- .. grid-item::
+ .. grid:: 1 1 2 2
+ :margin: 2 2 0 0
+ :gutter: 2
- .. figure:: media/Assembly/02_1M_Resistors.jpg
+ .. grid-item::
- **Step 2 - 1M Resistors**
+ .. figure:: media/Assembly/01_Bare_Board.*
+
+ **Step 1 - Bare Board**
+
+ .. grid-item::
+
+ .. figure:: media/Assembly/02_1M_Resistors.jpg
+
+ **Step 2 - 1M Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/03_330R_Resistors.jpg
+ .. figure:: media/Assembly/03_330R_Resistors.jpg
- **Step 3 - 330R Resistors**
+ **Step 3 - 330R Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/04_10K_Resistors.jpg
+ .. figure:: media/Assembly/04_10K_Resistors.jpg
- **Step 4 - 10K Resistors**
+ **Step 4 - 10K Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/05_22K_Resistors.jpg
+ .. figure:: media/Assembly/05_22K_Resistors.jpg
- **Step 5 - 22K Resistors**
+ **Step 5 - 22K Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/06_1K_Resistors.jpg
+ .. figure:: media/Assembly/06_1K_Resistors.jpg
- **Step 6 - 1K Resistors**
+ **Step 6 - 1K Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/07_220K_Resistors.jpg
+ .. figure:: media/Assembly/07_220K_Resistors.jpg
- **Step 7 - 220K Resistors**
+ **Step 7 - 220K Resistors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/08_1nF_Capacitors.jpg
+ .. figure:: media/Assembly/08_1nF_Capacitors.jpg
- **Step 8 - 1nF Capacitors**
+ **Step 8 - 1nF Capacitors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/09_100nF_Capacitors.jpg
+ .. figure:: media/Assembly/09_100nF_Capacitors.jpg
- **Step 9 - 100nF Capacitors**
+ **Step 9 - 100nF Capacitors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/10_100pF_Capacitors.jpg
+ .. figure:: media/Assembly/10_100pF_Capacitors.jpg
- **Step 10 - 100pF Capacitors**
+ **Step 10 - 100pF Capacitors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/11_Angled_Header_Pins.jpg
+ .. figure:: media/Assembly/11_Angled_Header_Pins.jpg
- **Step 11 - Angled Header Pins**
+ **Step 11 - Angled Header Pins**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/12_5x5mm_Buttons.jpg
+ .. figure:: media/Assembly/12_5x5mm_Buttons.jpg
- **Step 12 - 5x5mm Buttons**
+ **Step 12 - 5x5mm Buttons**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/13_OptoIsolator.jpg
+ .. figure:: media/Assembly/13_OptoIsolator.jpg
- **Step 13 - OptoIsolator**
+ **Step 13 - OptoIsolator**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/14_JST_PH_Angled_Connectors.jpg
+ .. figure:: media/Assembly/14_JST_PH_Angled_Connectors.jpg
- **Step 14 - JST PH Angled Connectors**
+ **Step 14 - JST PH Angled Connectors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/15_JST_PH_Straight_Connectors.jpg
+ .. figure:: media/Assembly/15_JST_PH_Straight_Connectors.jpg
- **Step 15 - JST PH Straight Connectors**
+ **Step 15 - JST PH Straight Connectors**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/16_IC_Socket.jpg
+ .. figure:: media/Assembly/16_IC_Socket.jpg
- **Step 16 - IC Socket**
+ **Step 16 - IC Socket**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/17_IC.jpg
+ .. figure:: media/Assembly/17_IC.jpg
- **Step 17 - IC**
+ **Step 17 - IC**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/18_LEDs.jpg
+ .. figure:: media/Assembly/18_LEDs.jpg
- **Step 18 - LEDs**
+ **Step 18 - LEDs**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/19_3.5mm_Headphone_Jack.jpg
+ .. figure:: media/Assembly/19_3.5mm_Headphone_Jack.jpg
- **Step 19 - 3.5mm Headphone Jack**
+ **Step 19 - 3.5mm Headphone Jack**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/20_2.2uF_Capacitor.jpg
+ .. figure:: media/Assembly/20_2.2uF_Capacitor.jpg
- **Step 20 - 2.2uF Capacitor**
+ **Step 20 - 2.2uF Capacitor**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/21_1uF_Capacitor.jpg
+ .. figure:: media/Assembly/21_1uF_Capacitor.jpg
- **Step 21 - 1uF Capacitor**
+ **Step 21 - 1uF Capacitor**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/22_470uF_Capacitor.jpg
+ .. figure:: media/Assembly/22_470uF_Capacitor.jpg
- **Step 22 - 470uF Capacitor**
+ **Step 22 - 470uF Capacitor**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/23_Header_Pins.jpg
+ .. figure:: media/Assembly/23_Header_Pins.jpg
- **Step 23 - Header Pins**
+ **Step 23 - Header Pins**
- .. grid-item::
+ .. grid-item::
- .. figure:: media/Assembly/24_Assembled.jpg
+ .. figure:: media/Assembly/24_Assembled.jpg
- **Step 24 - Assembled Shield**
+ **Step 24 - Assembled Shield**
-Still can't figure out the assembly? You can follow the video provided below to assemble your Shield.
+ Still can't figure out the assembly? You can follow the video provided below to assemble your Shield.
-.. youtube:: dcuCihh3yn4
- :width: 100%
+ .. youtube:: dcuCihh3yn4
+ :width: 100%
Using the Sensor
******************
@@ -288,7 +318,7 @@ Stack the Muscle BioAmp Shield on top of Arduino Uno properly.
.. only:: html
- .. figure:: media/gifs/shield-arduino-connection.gif
+ .. figure:: media/gifs/shield-arduino-connection.*
:align: center
.. only:: latex
@@ -303,7 +333,7 @@ Connect the BioAmp Cable to Muscle BioAmp Shield as shown.
.. only:: html
- .. figure:: media/gifs/electrode-cable-connection.gif
+ .. figure:: media/gifs/electrode-cable-connection.*
:align: center
.. only:: latex
@@ -340,20 +370,26 @@ Using gel electrodes
.. figure:: media/images/electrode-placement-1.*
:align: center
+ `Electrode placement for REF cable`
+
.. figure:: media/images/electrode-placement-2.*
:align: center
+ `Electrode placement for IN+, IN- cables`
+
Using Muscle BioAmp Band
---------------------------
1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.
2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -371,9 +407,11 @@ Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B
.. figure:: media/images/arduino-laptop-connection-1.*
:align: center
+ :width: 50%
.. figure:: media/images/arduino-laptop-connection-2.*
- :align: center
+ :align: center
+ :width: 50%
.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.
@@ -382,9 +420,9 @@ Step 6: Visualise EMG signals on laptop
Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
- EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
- EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Arduino Uno is connected. To find out the right COM port,
@@ -406,12 +444,14 @@ Now flex your arm to visualize the muscle signals in real time on your laptop.
.. figure:: media/images/visualise-emg.*
:align: center
+ `Visualise EMG signals on laptop`
+
Step 7: Visualise EMG signals on LEDs
==========================================
Copy paste the Arduino Sketch given below in Arduino IDE:
- LED Bar Graph: https://github.com/upsidedownlabs/BioAmp-EXG-Pill/blob/main/software/LEDBarGraph/LEDBarGraph.ino
+:fab:`github;pst-color-primary` `LED Bar Graph `_
Make sure you have selected the right board and COM port. Now upload the code, and flex your arm. You'll see the LED bar going up. More strength you apply, more the LED bar goes up.
@@ -425,6 +465,8 @@ Make sure you have selected the right board and COM port. Now upload the code, a
.. figure:: media/images/led-graph.*
:align: center
+ `Visualise EMG signals on LEDs`
+
Step 8: Listen to your EMG signals
====================================
@@ -447,6 +489,8 @@ Listening EMG on speakers
.. figure:: media/images/listening-emg-speakers.*
:align: center
+ Listening EMG on speakers
+
Listening EMG on a wired earphones/headphones
----------------------------------------------
@@ -464,6 +508,8 @@ Listening EMG on a wired earphones/headphones
.. figure:: media/images/listening-emg-earphones.*
:align: center
+ `Listening EMG on a wired earphones/headphones`
+
Step 9: Controlling a servo motor
===================================
@@ -471,7 +517,7 @@ Connect the servo claw to Muscle BioAmp Shield.
Copy paste the Arduino Sketch given below in Arduino IDE:
- Servo Controller: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/5_ServoControl/5_ServoControl.ino
+:fab:`github;pst-color-primary` `Servo Controller `_
Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time.
@@ -487,7 +533,7 @@ Connect the servo claw to Muscle BioAmp Shield.
Copy paste the Arduino Sketch given below in Arduino IDE:
- Claw Controller: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/tree/main/4_ClawController
+:fab:`github;pst-color-primary` `Claw Controller `_
Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time.
diff --git a/index.rst b/index.rst
index baa3f44c..db0c6c90 100644
--- a/index.rst
+++ b/index.rst
@@ -39,7 +39,7 @@ that you can use with our hardware.
.. grid-item::
.. card::
- :link: muscle_bioamp-biscute
+ :link: muscle-bioamp-biscute
:link-type: ref
:img-top: media/muscle-bioamp-biscute.*
:img-alt:
@@ -143,4 +143,11 @@ that you can use with our hardware.
:maxdepth: 1
:caption: Guides
- guides/index
\ No newline at end of file
+ guides/index
+
+.. toctree::
+ :hidden:
+ :maxdepth: 1
+ :caption: Courses
+
+ courses/index
\ No newline at end of file
diff --git a/kits/diy-neuroscience/basic/index.rst b/kits/diy-neuroscience/basic/index.rst
index 66fc290e..12288f4a 100644
--- a/kits/diy-neuroscience/basic/index.rst
+++ b/kits/diy-neuroscience/basic/index.rst
@@ -34,11 +34,17 @@ Software requirements
- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches in Maker UNO and visualise the data on your laptop.
-.. image:: media/arduino-ide.*
+.. figure:: media/arduino-ide.*
+ :align: center
+
+ Arduino IDE v1.8.19 (legacy IDE)
- Download Backyard Brains' `Spike Recorder `_ according to the operating system you are using (Windows, OSX, Linux).
-.. image:: media/byb.*
+.. figure:: media/byb.*
+ :align: center
+
+ BYB spike recorder
Using the kit
**************
@@ -48,7 +54,8 @@ This kit is made in a way so that even beginners can use it and get started with
Step 1 (optional): Configure for EMG/ECG
=========================================
-.. image:: media/configuration-emg-ecg.*
+.. figure:: media/configuration-emg-ecg.*
+ :align: center
BioAmp EXG Pill is by default configured for recording EEG or EOG, so if you are recording any of the two signals
you can skip this step. But if you want to record good quality ECG or EMG, then it is recommended to configure it
@@ -59,7 +66,8 @@ by making a solder joint as shown in the image above.
Step 2: Connect Maker UNO
==========================
-.. image:: media/connection-with-maker-uno.*
+.. figure:: media/connection-with-maker-uno.*
+ :align: center
Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Maker UNO via jumper cables provided by us. If you are connecting OUT to any other analog pin, then you will have to change the INPUT PIN in the arduino sketch accordingly.
@@ -68,7 +76,8 @@ Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0``
Step 3: Connecting electrode cable
===============================================
-.. image:: media/bioamp-cable.*
+.. figure:: media/bioamp-cable.*
+ :align: center
Connect the BioAmp cable to BioAmp EXG Pill by inserting the cable end in the JST PH connector as shown above.
@@ -80,7 +89,7 @@ Apply Nuprep Skin Preparation Gel on the skin surface where electrodes would be
For more information, please check out detailed step by step :ref:`skin-preparation`.
Step 5: Measuring EMG (ElectroMyoGraphy)
-===============================================
+===========================================
Electrodes placement
----------------------
@@ -93,18 +102,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or
2. Peel the plastic backing from electrodes
3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.
-.. image:: media/emg.*
+.. figure:: media/emg.*
+ :align: center
- **Using Muscle BioAmp Band:**
1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.
2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -113,9 +125,9 @@ Uploading the code
Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino
+:fab:`github;pst-color-primary` `EMG Filter `_
-EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino
+:fab:`github;pst-color-primary` `EMG Envelope `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Maker Uno is connected. To find out the right COM port,
@@ -132,7 +144,8 @@ Visualizing the EMG signals
Now flex your arm to visualize the muscle signals in real time on your laptop.
-.. image:: media/EMGEnvelop.*
+.. figure:: media/EMGEnvelop.*
+ :align: center
Step 6: Measuring ECG (ElectroCardioGraphy)
===============================================
@@ -148,7 +161,8 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or
2. Peel the plastic backing from electrodes
3. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side as shown in the diagram.
-.. image:: media/ecg.*
+.. figure:: media/ecg.*
+ :align: center
- **Using Heart BioAmp Band:**
@@ -156,18 +170,20 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or
2. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side.
3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.
-**Tutorial on how to use the band:**
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
-.. youtube:: fr5iORsVyUM
- :align: center
- :width: 100%
+ **Tutorial on how to use the band:**
+
+ .. youtube:: fr5iORsVyUM
+ :align: center
+ :width: 100%
Uploading the code
---------------------
Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:
-ECG Filter: https://github.com/upsidedownlabs/Heart-BioAmp-Arduino-Firmware/blob/main/2_ECGFilter/2_ECGFilter.ino
+:fab:`github;pst-color-primary` `ECG Filter `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Maker Uno is connected. To find out the right COM port,
@@ -182,7 +198,8 @@ After opening the serial plotter make sure to select the baud rate to 115200.
Visualizing the ECG signals
-----------------------------
-.. image:: media/bioamp-Exg-Pill-ECG.*
+.. figure:: media/bioamp-Exg-Pill-ECG.*
+ :align: center
Step 7: Measuring EOG (ElectroOculoGraphy)
=============================================
@@ -194,7 +211,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move
- **Horizontal EOG recording:**
-.. image:: media/eog-horizontal.*
+.. figure:: media/eog-horizontal.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -202,7 +220,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move
- **Vertical EOG recording:**
-.. image:: media/eog-vertical.*
+.. figure:: media/eog-vertical.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -213,7 +232,7 @@ Uploading the code
Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:
-EOG Filter: https://github.com/upsidedownlabs/Eye-BioAmp-Arduino-Firmware/blob/main/2_EOGFilter/2_EOGFilter.ino
+:fab:`github;pst-color-primary` `EOG Filter `_
Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu,
select the COM port on which your Maker Uno is connected. To find out the right COM port,
@@ -228,7 +247,8 @@ After opening the serial plotter make sure to select the baud rate to 115200.
Visualizing the EOG signals
------------------------------
-.. image:: media/bioamp-exg-pill-eog.*
+.. figure:: media/bioamp-exg-pill-eog.*
+ :align: center
Step 8: Measuring EEG (ElectroEncephaloGraphy)
===============================================
@@ -236,7 +256,8 @@ Step 8: Measuring EEG (ElectroEncephaloGraphy)
Let's understand the electrode placements before moving forward in this project. For recording EEG from
different parts of the brain, you have to place the electrodes according to the `International 10-20 system for recording EEG `_.
-.. image:: media/10-20-system.*
+.. figure:: media/10-20-system.*
+ :align: center
:width: 80%
Electrodes placement
@@ -246,7 +267,8 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or
- **Using gel electrodes to record from prefrontal cortex part of brain:**
-.. image:: media/eeg.*
+.. figure:: media/eeg.*
+ :align: center
1. Connect the BioAmp cable to gel electrodes.
2. Peel the plastic backing from electrodes.
@@ -260,11 +282,13 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or
.. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same.
-**Tutorial on how to use the band:**
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
-.. youtube:: O6qp7teT-sM
- :align: center
- :width: 100%
+ **Tutorial on how to use the band:**
+
+ .. youtube:: O6qp7teT-sM
+ :align: center
+ :width: 100%
Uploading the code
-----------------------
@@ -287,6 +311,7 @@ Open up your BackyardBrains Spike Recorder software. At first, it will monitor s
the :fas:`gear` icon on the top left corner of the screen, select the COM port on which the Maker UNO is connected and click on connect.
.. figure:: media/spike-recorder-configurations.*
+ :align: center
Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should
set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between
@@ -295,6 +320,10 @@ these frequencies.
Now everything is configured and connected. So close the settings window and start recording EEG signals.
.. figure:: media/bioamp-exg-pill-eeg.*
+ :align: center
+ :alt: Recording EEG from pre-frontal cortex part of brain
+
+ Recording EEG signals from pre-frontal cortex
The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin.
diff --git a/kits/diy-neuroscience/pro/index.rst b/kits/diy-neuroscience/pro/index.rst
index 813f34a7..2c5399bc 100644
--- a/kits/diy-neuroscience/pro/index.rst
+++ b/kits/diy-neuroscience/pro/index.rst
@@ -12,6 +12,8 @@ applications, and gain valuable insights.
.. figure:: media/diy-neuroscience-kit-pro.*
:align: center
+ DIY Neuroscience Kit Pro
+
Contents of the kit
********************
@@ -45,6 +47,8 @@ Contents of the kit
.. figure:: media/kit-content.*
:align: center
+Click on the link below to see the unboxing of the kit:
+
.. youtube:: Sn389Q7Izy4
:width: 100%
:align: center
@@ -62,7 +66,7 @@ Download the following according to the operating system you are using (Windows,
- `Arduino IDE v1.8.19 (legacy IDE) `_
-.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
+.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.*
Using the kit
**************
@@ -84,7 +88,7 @@ just a few. It also works with any dedicated ADC, like the Texas Instruments ADS
.. figure:: ../../../media/bioamp-exg-pill.*
-.. note:: Checkout the complete documentation on `BioAmp EXG Pill `_ which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it.
+.. note:: Checkout the complete documentation on :ref:`bioamp-exg-pill` which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it.
Step 2: Using Muscle BioAmp Shield
=======================================
@@ -96,7 +100,7 @@ signals to make amazing projects in the domain of Human-Computer Interface (HCI)
.. figure:: ../../../media/muscle-bioamp-shield.*
-.. note:: Checkout the complete documentation on `Muscle BioAmp Shield `_ which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it.
+.. note:: Checkout the complete documentation on :ref:`muscle-bioamp-shield` which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it.
Step 3: Using the sensors together
======================================
@@ -112,14 +116,16 @@ a. Connecting Muscle BioAmp Shield to MCU/ADC
Stack the Muscle BioAmp Shield on top of your Arduino Uno properly.
-.. only:: html
+.. only:: latex
- .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/gifs/shield-arduino-connection.gif
+ .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/images/shield-arduino-connection.*
:align: center
-.. only:: latex
+ Stacking Muscle BioAmp Shield on top of Arduino
- .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/images/shield-arduino-connection.*
+.. only:: html
+
+ .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/gifs/shield-arduino-connection.gif
:align: center
b. Configure for ECG/EMG (optional)
@@ -130,8 +136,9 @@ BioAmp EXG Pill is by default configured for recording EEG or EOG but if you wan
.. figure:: ../../../hardware/bioamp/bioamp-exg-pill/media/assembly-step2.*
:align: center
-.. note:: Even without making the solder joint the BioAmp EXG Pill is capable of recording ECG or EMG but the signals would be more accurate if you configure it.
+ Configure BioAmp EXG Pill for EMG/ECG
+.. note:: Even without making the solder joint the BioAmp EXG Pill is capable of recording ECG or EMG but the signals would be more accurate if you configure it.
c. Connecting sensors together
--------------------------------------
@@ -148,16 +155,39 @@ Connect the BioAmp EXG Pill to the A2 port of Muscle BioAmp Shield via 3-pin STE
| A2 | OUT |
+----------------------+-----------------+
-.. figure:: media/gifs/shield-pill-connection.*
- :align: center
+.. only:: latex
+
+ .. figure:: media/images/shield-pill-connection.*
+ :align: center
+
+ Inserting JST PH connector in A2 port of Muscle BioAmp Shield
+
+ .. figure:: media/images/shield-pill-connection-2.*
+ :align: center
+
+ Muscle BioAmp Shield to BioAmp EXG Pill connections
+
+.. only:: html
+
+ .. figure:: media/gifs/shield-pill-connection.*
+ :align: center
d. Connecting electrode cables
--------------------------------
Connect one BioAmp cable to BioAmp EXG Pill and another BioAmp cable to Muscle BioAmp Shield by inserting the cable ends into the respective JST PH connectors as shown below:
-.. figure:: media/gifs/bioamp-cables-connection.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/bioamp-cables-connection.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/images/bioamp-cables-connection.*
+ :align: center
+
+ Connecting BioAmp Cables to the sensors
e. Skin Preparation
---------------------------
@@ -166,7 +196,7 @@ We'll create a 2-channel EMG acquisition system and to do so, we'll be using bot
Apply Nuprep Skin Preparation Gel on the skin surface where electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.
-For more information, please check out detailed step by step `skin preparation guide `_.
+For more information, please check out detailed step by step :ref:`skin-preparation`.
f. Electrodes placement
-------------------------
@@ -180,36 +210,60 @@ Using gel electrodes
2. Peel the plastic backing from electrodes.
3. Place the IN+ and IN- cables on the left arm near the ulnar nerve & REF (reference) at the back of your left hand as shown below.
-.. figure:: media/gifs/gel-electrodes-connection.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/gel-electrodes-connection.*
+ :align: center
4. Now snap the BioAmp Cable connected to Muscle BioAmp Shield to gel electrodes.
5. Peel the plastic backing from electrodes.
6. Place the IN+ and IN- cables on the right arm near the ulnar nerve & REF (reference) at the back of your right hand as shown below.
-.. figure:: media/gifs/gel-electrodes-connection-2.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/gel-electrodes-connection-2.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/images/gel-electrodes-connection.*
+ :align: center
+
+ Gel electrodes placement
Using Muscle BioAmp Band
+++++++++++++++++++++++++
1. Snap the BioAmp Cable connected to BioAmp EXG Pill on Muscle BioAmp Band in a way such that IN+ and IN- are placed on the left arm near the ulnar nerve & REF (reference) on the far side of the band.
-.. figure:: media/gifs/bioamp-band-connection-2.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/bioamp-band-connection-2.*
+ :align: center
2. Snap the BioAmp Cable connected to Muscle BioAmp Shield on Muscle BioAmp Band in a way such that IN+ and IN- are placed on the right arm near the ulnar nerve & REF (reference) on the far side of the band.
-.. figure:: media/gifs/bioamp-band-connection.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/bioamp-band-connection.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/images/bioamp-band-connection.*
+ :align: center
+
+ Muscle BioAmp Band placement
3. Now put a small drop of electrode gel between the skin and metallic parts of BioAmp Cables to get the best results.
+.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below.
+
**Tutorial on how to use the band:**
-.. youtube:: xYZdw0aesa0
- :align: center
- :width: 100%
+ .. youtube:: xYZdw0aesa0
+ :align: center
+ :width: 100%
.. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.
@@ -217,8 +271,8 @@ g. Uploading the code
----------------------
Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Download the github repository given below:
-
-Muscle BioAmp Arduino Firmware: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/
+
+:fab:`github;pst-color-primary` `Muscle BioAmp Arduino Firmware `_
Go to the folder ``8_EMGScrolling``, open the arduino sketch ``8_EMGScrolling.ino`` in Arduino IDE.
@@ -236,13 +290,42 @@ Go to ``tools`` from the menu bar, click on ``serial monitor`` to open it or cli
Press the ``SW1 button`` on Muscle BioAmp Shield. Now you'll see green LED glowing on the LED bar. When you flex your right arm, you'll get output value 1 on the serial monitor and red LED will glow. Similarly, when you flex your left arm, you'll get output value 2 and yellow LED will glow.
-.. figure:: media/gifs/testing.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/testing.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/images/testing-1.*
+ :align: center
+
+ Press the SW1 button to start getting the output
+
+ .. figure:: media/images/testing-2.*
+ :align: center
+
+ Flex the right arm, red LED glows
+
+ .. figure:: media/images/testing-3.*
+ :align: center
+
+ Flex the left arm, yellow LED glows
+
+ .. figure:: media/images/testing-4.*
+ :align: center
+
+ Flex the right arm, serial monitor shows output value 1
+
+ .. figure:: media/images/testing-5.*
+ :align: center
+
+ Flex the left arm, serial monitor shows output value 2
i. Running python script
-------------------------
-Open Visual Studio Code, click on File < Open folder to open the folder ``8_EMGScrolling``.
+Open Visual Studio Code, click on File > Open folder to open the folder ``8_EMGScrolling``.
Open the terminal, and ensure that the path is configured to the location of the ``requirement.txt`` file.
@@ -269,15 +352,26 @@ Run the Python script ``EMG_Scroll.py`` by writing the given command in the term
j. Scrolling using EMG signals
---------------------------------
+Press the ``SW1 button`` on Muscle BioAmp Shield again.
+
In the terminal, you will see Move Now prompt. When you flex your right arm, you'll see UP in the terminal. Similarly, when you move your left arm, you'll see DOWN in the terminal.
-.. figure:: media/gifs/demo-1.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/demo-1.*
+ :align: center
+
+.. only:: latex
+
+ .. figure:: media/images/demo-1.*
+ :align: center
Now, open youtube shorts on your laptop and start scrolling using your muscle signals.
-.. figure:: media/gifs/demo-2.*
- :align: center
+.. only:: html
+
+ .. figure:: media/gifs/demo-2.*
+ :align: center
.. note:: What's happening in the background? Whenever an EMG signal is detected, it acts as a trigger to emulate UP or DOWN key on the keyboard.
@@ -286,7 +380,7 @@ k. Calibrating the code
**Changes in Arduino Sketch**
-Modify the threshold values on lines 73 and 74. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill.
+Modify the threshold values on **lines 73 and 74**. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill.
Uncomment line 71 in the Arduino code and navigate to Tools > Serial Plotter. You’ll see two plots showing the EMG signals of both of your arms. Flex your right arm and observe the peak value on the y-axis. If the peak value is around 240, you can set threshold 1 anywhere between 150 to 200. The lower the threshold value, the easier it is to trigger the output as UP or DOWN, and vice versa. Repeat the process to determine the threshold 2 value for your left arm.
@@ -294,7 +388,7 @@ After setting the thresholds, comment out line 71.
**Changes in Python script**
-Adjust the latency value on line 51. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily.
+Adjust the latency value on **line 51**. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily.
l. Conclusion
-----------------
@@ -365,7 +459,7 @@ Some project ideas
:text-align: center
:link: https://www.instructables.com/Tracking-UP-and-DOWN-Movements-of-Eyes-Using-EOG/
- 2. Projects made using Muscle BioAmp Shield
+ 1. Projects made using Muscle BioAmp Shield
=============================================
.. grid:: 2 2 2 2
@@ -392,7 +486,7 @@ Some project ideas
:text-align: center
:link: https://www.instructables.com/Making-a-Muscle-Strength-Game-Using-Muscle-BioAmp-/
- 3. Projects made using the sensors together
+ 1. Projects made using the sensors together
==============================================
.. grid:: 2 2 2 2
@@ -410,3 +504,39 @@ Some project ideas
These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and
Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech.
+.. only:: latex
+
+ You can find step-by-step tutorials for various HCI/BCI projects on our `Instructables `_.
+
+ Projects made using BioAmp EXG Pill
+ ====================================
+
+ 1. `Controlling video game using brainwaves (EEG) `_
+ 2. `Visualising electrical impulses from eyes (EOG) `_
+ 3. `Recording EEG from visual cortex part of brain `_
+ 4. `Recording EEG from prefrontal cortex part of brain `_
+ 5. `Eye blink detection `_
+ 6. `Creating a drowsiness detector `_
+ 7. `Record publication-grade ECG `_
+ 8. `Measuring heart rate `_
+ 9. `Detecting heart beats `_
+ 10. `Record publication-grade EMG `_
+ 11. `Detecting up and down movement of eyes `_
+
+ Projects made using Muscle BioAmp Shield
+ ===========================================
+
+ 1. `Record, visualise, and listen to EMG signals `_
+ 2. `Controlling 3d-printed servo claw using EMG `_
+ 3. `Controlling prosthetic hand using EMG `_
+ 4. `Building the ultimate servo claw game `_
+ 5. `Building muscle strength game `_
+
+ Projects made using the sensors together
+ ============================================
+
+ 1. `Control dino game using eye blinks `_
+ 2. `Control servo claw using EOG `_
+
+ These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and
+ Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech
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