""" LIF Neuron Visualizer Usage: python3 visualizer.py /dev/cu.usbmodem1101 """ import sys import serial import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec import matplotlib.path as mpath import matplotlib.patches as mpatches from matplotlib.animation import FuncAnimation from matplotlib.patches import Circle, Ellipse, PathPatch from collections import deque import numpy as np PORT = sys.argv[1] if len(sys.argv) > 1 else "/dev/cu.usbmodem1101" BAUD = 115200 WINDOW = 400 ser = serial.Serial(PORT, BAUD, timeout=0.05) # Biological scale V_REST_MV = -70.0 V_THRESH_MV = -55.0 V_SPIKE_MV = 40.0 I_MAX_PA = 500.0 def to_mv(v_norm): return V_REST_MV + (v_norm / 0.7) * (V_THRESH_MV - V_REST_MV) def to_pa(i_norm): return i_norm * I_MAX_PA # Data buffers count = 0 xs = deque(maxlen=WINDOW) voltages_mv = deque(maxlen=WINDOW) currents_pa = deque(maxlen=WINDOW) spike_xs = deque(maxlen=50) spike_count = 0 # Colors plt.style.use("dark_background") BG = "#060612" CYAN = "#00e5ff" GREEN = "#00e676" RED = "#ff1744" ORANGE = "#ff9100" GREY = "#333333" WHITE = "#e0e0e0" PURPLE = "#b388ff" # --- Layout: neuron on top (big), plots below --- fig = plt.figure(figsize=(14, 9), facecolor=BG) gs = gridspec.GridSpec(3, 2, height_ratios=[3, 1.8, 1.8], hspace=0.3, wspace=0.25) ax_neuron = fig.add_subplot(gs[0, :], facecolor=BG) ax_v = fig.add_subplot(gs[1, :], facecolor=BG) ax_i = fig.add_subplot(gs[2, :], facecolor=BG, sharex=ax_v) # ============================================================ # NEURON DIAGRAM (organic, curved, big) # ============================================================ ax_neuron.set_xlim(-8, 10) ax_neuron.set_ylim(-4.5, 4.5) ax_neuron.set_aspect("equal") ax_neuron.axis("off") def organic_curve(pts, num=40): """Smooth a set of points into a natural curve using cubic interpolation.""" pts = np.array(pts) t = np.linspace(0, 1, len(pts)) t_smooth = np.linspace(0, 1, num) x_smooth = np.interp(t_smooth, t, pts[:, 0]) y_smooth = np.interp(t_smooth, t, pts[:, 1]) # add slight organic wobble x_smooth += np.sin(t_smooth * np.pi * 3) * 0.03 y_smooth += np.cos(t_smooth * np.pi * 2.5) * 0.03 return x_smooth, y_smooth def draw_branch(ax, pts, base_width=2.0, color=GREEN, base_alpha=0.5): """Draw a tapered organic branch.""" x, y = organic_curve(pts, 30) n = len(x) lines = [] for i in range(n - 1): frac = i / n w = base_width * (1 - 0.7 * frac) a = base_alpha * (1 - 0.4 * frac) l, = ax.plot([x[i], x[i+1]], [y[i], y[i+1]], color=color, linewidth=w, alpha=a, solid_capstyle="round") lines.append(l) return lines # -- Dendrite trees (left side, organic branching) -- dendrite_lines = [] # upper dendrite trunk dendrite_lines += draw_branch(ax_neuron, [(-1.8, 0.4), (-2.8, 1.0), (-3.5, 1.8), (-4.2, 2.8)], base_width=3.0) # upper sub-branches dendrite_lines += draw_branch(ax_neuron, [(-3.2, 1.5), (-3.8, 2.5), (-4.5, 3.2)], base_width=1.5) dendrite_lines += draw_branch(ax_neuron, [(-3.5, 1.8), (-4.4, 2.0), (-5.2, 2.5)], base_width=1.2) dendrite_lines += draw_branch(ax_neuron, [(-4.2, 2.8), (-4.8, 3.5)], base_width=1.0) dendrite_lines += draw_branch(ax_neuron, [(-4.2, 2.8), (-5.0, 3.0)], base_width=0.8) dendrite_lines += draw_branch(ax_neuron, [(-3.8, 2.5), (-4.0, 3.3)], base_width=0.7) dendrite_lines += draw_branch(ax_neuron, [(-5.2, 2.5), (-5.8, 3.0)], base_width=0.6) dendrite_lines += draw_branch(ax_neuron, [(-5.2, 2.5), (-5.6, 2.2)], base_width=0.5) # middle dendrite dendrite_lines += draw_branch(ax_neuron, [(-1.8, 0.0), (-3.0, 0.1), (-4.0, -0.2), (-5.0, 0.3)], base_width=2.5) dendrite_lines += draw_branch(ax_neuron, [(-4.0, -0.2), (-4.8, -0.8), (-5.5, -0.5)], base_width=1.2) dendrite_lines += draw_branch(ax_neuron, [(-5.0, 0.3), (-5.8, 0.8)], base_width=0.8) dendrite_lines += draw_branch(ax_neuron, [(-5.0, 0.3), (-5.7, 0.0)], base_width=0.6) # lower dendrite trunk dendrite_lines += draw_branch(ax_neuron, [(-1.8, -0.4), (-2.8, -1.0), (-3.5, -1.8), (-4.2, -2.8)], base_width=3.0) dendrite_lines += draw_branch(ax_neuron, [(-3.2, -1.5), (-3.8, -2.5), (-4.5, -3.2)], base_width=1.5) dendrite_lines += draw_branch(ax_neuron, [(-3.5, -1.8), (-4.4, -2.0), (-5.2, -2.5)], base_width=1.2) dendrite_lines += draw_branch(ax_neuron, [(-4.2, -2.8), (-4.8, -3.5)], base_width=1.0) dendrite_lines += draw_branch(ax_neuron, [(-4.2, -2.8), (-5.0, -3.0)], base_width=0.8) dendrite_lines += draw_branch(ax_neuron, [(-5.2, -2.5), (-5.8, -2.8)], base_width=0.5) # -- Synapse boutons on dendrite tips -- synapse_dots = [] tip_positions = [ (-4.8, 3.5), (-5.0, 3.0), (-4.0, 3.3), (-5.8, 3.0), (-5.6, 2.2), (-5.8, 0.8), (-5.7, 0.0), (-5.5, -0.5), (-4.8, -3.5), (-5.0, -3.0), (-4.5, -3.2), (-5.8, -2.8), ] for tx, ty in tip_positions: d = Circle((tx, ty), 0.12, facecolor=GREEN, edgecolor=GREEN, alpha=0.3, linewidth=0.5) ax_neuron.add_patch(d) synapse_dots.append(d) # -- Soma (irregular blob, not a perfect circle) -- # create organic soma shape theta = np.linspace(0, 2 * np.pi, 80) r_soma = 1.4 + 0.15 * np.sin(3 * theta) + 0.1 * np.cos(5 * theta) + 0.08 * np.sin(7 * theta) soma_x = r_soma * np.cos(theta) soma_y = r_soma * np.sin(theta) * 0.95 # slightly squished soma_verts = list(zip(soma_x, soma_y)) soma_verts.append(soma_verts[0]) soma_codes = [mpath.Path.MOVETO] + [mpath.Path.LINETO] * (len(soma_verts) - 2) + [mpath.Path.CLOSEPOLY] soma_path = mpath.Path(soma_verts, soma_codes) soma = PathPatch(soma_path, facecolor=(0, 0.1, 0.2, 0.4), edgecolor=CYAN, linewidth=2.5) ax_neuron.add_patch(soma) # nucleus (off-center, organic) theta_n = np.linspace(0, 2 * np.pi, 50) r_nuc = 0.5 + 0.05 * np.sin(4 * theta_n) nuc_x = 0.1 + r_nuc * np.cos(theta_n) nuc_y = 0.15 + r_nuc * np.sin(theta_n) * 0.85 nuc_verts = list(zip(nuc_x, nuc_y)) nuc_verts.append(nuc_verts[0]) nuc_codes = [mpath.Path.MOVETO] + [mpath.Path.LINETO] * (len(nuc_verts) - 2) + [mpath.Path.CLOSEPOLY] nuc_path = mpath.Path(nuc_verts, nuc_codes) nucleus = PathPatch(nuc_path, facecolor=(0.05, 0.12, 0.25, 0.6), edgecolor=PURPLE, linewidth=1.2) ax_neuron.add_patch(nucleus) # nucleolus (tiny dot inside nucleus) nucleolus = Circle((0.15, 0.2), 0.13, facecolor=PURPLE, alpha=0.3, edgecolor="none") ax_neuron.add_patch(nucleolus) # -- Axon hillock (tapered transition from soma to axon) -- hillock_x = [1.3, 1.6, 2.0, 2.3] hillock_y_top = [0.5, 0.35, 0.25, 0.2] hillock_y_bot = [-0.5, -0.35, -0.25, -0.2] ax_neuron.fill_between(hillock_x, hillock_y_bot, hillock_y_top, color=(0, 0.1, 0.2, 0.3), edgecolor=CYAN, linewidth=1.2) # -- Axon (long, with organic waviness) -- axon_t = np.linspace(0, 1, 100) axon_x = 2.3 + axon_t * 6.5 axon_y = np.sin(axon_t * np.pi * 4) * 0.08 # slight wave ax_neuron.plot(axon_x, axon_y, color=ORANGE, linewidth=2.0, alpha=0.5, solid_capstyle="round") # -- Myelin sheaths (rounded organic capsules, not boxes) -- myelin_patches = [] myelin_positions = [3.0, 4.2, 5.4, 6.6] for mx in myelin_positions: # draw as a rounded ellipse m = Ellipse((mx, 0), 0.8, 0.55, facecolor=(0.15, 0.1, 0, 0.25), edgecolor=ORANGE, linewidth=1.2, alpha=0.6) ax_neuron.add_patch(m) myelin_patches.append(m) # nodes of ranvier labels (gaps between myelin) for i in range(len(myelin_positions) - 1): gap_x = (myelin_positions[i] + myelin_positions[i+1]) / 2 ax_neuron.plot(gap_x, 0, "o", color=CYAN, markersize=3, alpha=0.3) # -- Axon terminals (synaptic boutons) -- terminal_positions = [(8.2, 0.6), (8.5, 0.0), (8.2, -0.6)] terminals = [] for tx, ty in terminal_positions: # branch from axon tip ax_neuron.plot([7.8, tx], [0, ty], color=ORANGE, linewidth=1.2, alpha=0.4) t = Circle((tx, ty), 0.2, facecolor=BG, edgecolor=RED, linewidth=2, alpha=0.5) ax_neuron.add_patch(t) terminals.append(t) # vesicles inside terminals for tx, ty in terminal_positions: for vx, vy in [(tx-0.05, ty+0.05), (tx+0.06, ty-0.04), (tx-0.02, ty-0.06)]: v = Circle((vx, vy), 0.04, facecolor=RED, alpha=0.2, edgecolor="none") ax_neuron.add_patch(v) # -- Spike ring (hidden, expands on spike) -- spike_ring = Circle((0, 0), 1.8, fill=False, edgecolor=RED, linewidth=0, alpha=0) ax_neuron.add_patch(spike_ring) # -- Labels -- ax_neuron.text(-5.5, 4.0, "dendrites", ha="center", color=GREEN, fontsize=8, alpha=0.5, style="italic") ax_neuron.text(0, -2.2, "soma", ha="center", color=CYAN, fontsize=8, alpha=0.4, style="italic") ax_neuron.text(0.15, 0.55, "nucleus", ha="center", color=PURPLE, fontsize=6, alpha=0.4) ax_neuron.text(4.8, -0.9, "myelin sheath", ha="center", color=ORANGE, fontsize=7, alpha=0.4, style="italic") ax_neuron.text(1.7, -0.9, "axon hillock", ha="center", color=CYAN, fontsize=6, alpha=0.35, style="italic") ax_neuron.text(8.5, -1.3, "synaptic\nterminals", ha="center", color=RED, fontsize=7, alpha=0.4, style="italic") # voltage readout inside soma v_text = ax_neuron.text(0, -0.3, "-70 mV", ha="center", va="center", color=CYAN, fontsize=16, fontweight="bold", family="monospace") # input current label near dendrites i_text = ax_neuron.text(-5.5, -4.0, "0 pA", ha="center", color=GREEN, fontsize=11, fontweight="bold", family="monospace") # ============================================================ # PLOTS # ============================================================ line_v, = ax_v.plot([], [], color=CYAN, linewidth=1.5, alpha=0.9) ax_v.axhline(y=V_THRESH_MV, color=RED, linestyle="--", linewidth=1, alpha=0.4) ax_v.axhline(y=V_REST_MV, color=GREY, linestyle=":", linewidth=0.8, alpha=0.3) ax_v.set_ylabel("Membrane (mV)", color=WHITE, fontsize=9) ax_v.set_ylim(-78, 50) ax_v.tick_params(colors=GREY, labelsize=7) for s in ["top", "right"]: ax_v.spines[s].set_visible(False) for s in ["bottom", "left"]: ax_v.spines[s].set_color(GREY) ax_v.text(0.01, 0.9, "V_mem", transform=ax_v.transAxes, color=CYAN, fontsize=8, fontweight="bold", alpha=0.4) ax_v.text(0.99, 0.82, f"{V_THRESH_MV:.0f} mV", transform=ax_v.transAxes, color=RED, fontsize=7, alpha=0.35, ha="right") line_i, = ax_i.plot([], [], color=GREEN, linewidth=1.5, alpha=0.9) ax_i.set_ylabel("I_syn (pA)", color=WHITE, fontsize=9) ax_i.set_ylim(-10, I_MAX_PA + 30) ax_i.set_xlabel("samples (10 ms each)", color=GREY, fontsize=8) ax_i.tick_params(colors=GREY, labelsize=7) for s in ["top", "right"]: ax_i.spines[s].set_visible(False) for s in ["bottom", "left"]: ax_i.spines[s].set_color(GREY) ax_i.text(0.01, 0.85, "I_syn", transform=ax_i.transAxes, color=GREEN, fontsize=8, fontweight="bold", alpha=0.4) # Title fig.text(0.5, 0.975, "Leaky Integrate-and-Fire Neuron", ha="center", color=WHITE, fontsize=15, fontweight="bold") fig.text(0.5, 0.955, "XIAO ESP32-S3 \u2502 EC11 Rotary Encoder \u2502 \u03C4 = 2.2s \u2502 V_thresh = -55 mV", ha="center", color=GREY, fontsize=8) fill_collection = None spike_fade = 0 def update(frame): global count, spike_count, fill_collection, spike_fade new_spikes = 0 for _ in range(30): raw = ser.readline() if not raw: break try: parts = raw.decode("utf-8", errors="ignore").strip().split(",") if len(parts) != 4: continue i_in = float(parts[1]) v = float(parts[2]) sp = int(parts[3]) xs.append(count) if sp == 1: voltages_mv.append(V_SPIKE_MV) spike_xs.append(count) spike_count += 1 new_spikes += 1 else: voltages_mv.append(to_mv(v)) currents_pa.append(to_pa(i_in)) count += 1 except (ValueError, IndexError): continue if len(xs) < 2: return [] x = list(xs) v_list = list(voltages_mv) i_list = list(currents_pa) line_v.set_data(x, v_list) line_i.set_data(x, i_list) if fill_collection is not None: fill_collection.remove() fill_clipped = [max(v, V_REST_MV) for v in v_list] fill_collection = ax_v.fill_between(x, V_REST_MV, fill_clipped, color=CYAN, alpha=0.05) ax_v.set_xlim(x[0], x[-1]) ax_i.set_xlim(x[0], x[-1]) cur_v = v_list[-1] cur_i = i_list[-1] cur_v_norm = max(0, min((cur_v - V_REST_MV) / (V_THRESH_MV - V_REST_MV), 1.0)) i_frac = min(cur_i / I_MAX_PA, 1.0) # --- Soma glow --- r = cur_v_norm * 0.8 g = 0.08 + 0.08 * (1 - cur_v_norm) b = 0.25 + 0.55 * (1 - cur_v_norm) soma.set_facecolor((r, g, b, 0.4 + 0.3 * cur_v_norm)) soma.set_edgecolor(RED if cur_v_norm > 0.85 else CYAN) soma.set_linewidth(2.5 + 4 * cur_v_norm) # --- Dendrite glow --- for d in synapse_dots: d.set_alpha(0.15 + 0.85 * i_frac) d.set_radius(0.08 + 0.08 * i_frac) for l in dendrite_lines: l.set_alpha(min(1.0, l.get_alpha() * 0.5 + 0.5 * (0.3 + 0.6 * i_frac))) # --- Voltage text --- v_text.set_text(f"{cur_v:+.0f} mV") v_text.set_color(RED if cur_v_norm > 0.85 else CYAN) v_text.set_fontsize(16 + 4 * cur_v_norm) # --- Input text --- i_text.set_text(f"{cur_i:.0f} pA") i_text.set_alpha(0.4 + 0.6 * i_frac) # --- Spike animation --- if new_spikes > 0: spike_fade = 10 if spike_fade > 0: a = spike_fade / 10.0 # soma flash soma.set_facecolor((1, 0.15, 0.05, 0.5 + 0.4 * a)) soma.set_edgecolor((1, 0.3, 0.1)) soma.set_linewidth(3 + 5 * a) # spike ring expands spike_ring.set_linewidth(3 * a) spike_ring.set_alpha(a * 0.6) spike_ring.set_radius(1.8 + (10 - spike_fade) * 0.3) # terminals flash for t in terminals: t.set_facecolor((1, 0.1, 0.1, a * 0.8)) t.set_edgecolor((1, 0.3, 0.1)) # myelin flash for m in myelin_patches: m.set_facecolor((0.4, 0.2, 0, 0.3 * a)) m.set_edgecolor((1, 0.6, 0, a)) spike_fade -= 1 else: spike_ring.set_linewidth(0) spike_ring.set_alpha(0) for t in terminals: t.set_facecolor(BG) t.set_edgecolor(RED) t.set_alpha(0.5) for m in myelin_patches: m.set_facecolor((0.15, 0.1, 0, 0.25)) m.set_edgecolor(ORANGE) m.set_alpha(0.6) # --- Firing rate --- recent = sum(1 for sx in spike_xs if sx > count - 200) rate_hz = recent / (200 * 0.01) if count > 200 else 0 # title area firing info fig.texts[-1].set_text( f"XIAO ESP32-S3 \u2502 EC11 Rotary Encoder \u2502 \u03C4 = 2.2s \u2502 " f"Spikes: {spike_count} \u2502 Rate: {rate_hz:.1f} Hz" f"{' \u26a1' if new_spikes > 0 else ''}" ) return [] ani = FuncAnimation(fig, update, interval=40, blit=False, cache_frame_data=False) plt.subplots_adjust(top=0.94, bottom=0.05, left=0.06, right=0.97, hspace=0.3) plt.show() ser.close()