DD014.1: Visual Rendering Specification for Multi-Scale Visualization

• Status: Proposed
• Author: OpenWorm Core Team
• Date: 2026-02-16
• Companion to: DD014 (Dynamic Visualization and Multi-Scale Exploration Architecture)
• Related: DD001 (Neural Circuit), DD002 (Muscle Model), DD003 (Body Physics), DD004 (Cell Identity), DD005 (Cell-Type Specialization), DD006 (Neuropeptidergic Connectome), DD007 (Pharyngeal System), DD008 (Data Integration), DD009 (Intestinal Oscillator), DD010 (Validation Framework)

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Phase: Phase 1 | Layer: Visualization

TL;DR

This document defines what the OpenWorm simulation looks like — exact colors, materials, lighting, transparency, transitions, and rendering algorithms for every visual element at every scale. DD014 specifies the architecture (data pipeline, Zarr schema, Trame/Three.js framework, Docker integration); DD014.1 specifies the visual design. A developer should be able to implement any visual element by reading DD014.1 (appearance) and DD014 (data format) without guessing.

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Goal & Success Criteria

1. Implementation-complete visual spec. A developer working in Three.js, PyVista, or any WebGPU renderer can implement any visual element described here without asking "what color?" or "how bright?" or "how transparent?"
2. Canonical color palette. Every one of the 959 cells in the C. elegans organism has a defined color assignment, either directly (for the 37 Virtual Worm material categories) or by inheritance (cell → tissue type → material category).
3. Reference mockups as acceptance test. 14 canonical views define "correct" rendering. Visual review of implementation screenshots against these mockup specifications is the acceptance test.
4. Multi-scale continuity. Transitions between organism, tissue, and molecular scales are specified with enough detail to implement smooth, non-jarring zoom animations.

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Deliverables

• Canonical color palette definition (hex values for all 37 Virtual Worm material categories, activity-state dynamic colors, and molecular-scale palette)
• 14 reference mockup specifications as acceptance criteria (Sections 6, Mockups 1-14)
• Rendering technique specifications (ambient occlusion, subsurface scattering parameters, OIT, bloom)
• Cell-to-material mapping rules for all 959 cells (Section 7)
• Theme/style configuration file (JSON/YAML) for the DD014 viewer [TO BE CREATED]

Repository & Issues

• Primary repository: openworm/viewer [TO BE CREATED] (rendering configuration and theme files)
• Issue label: dd014.1, rendering
• Related: DD014 parent DD (viewer architecture)

How to Build & Test

• Prerequisites: DD014 viewer running locally (see DD014)
• Test procedure: Load reference scene, compare implementation screenshots against the 14 mockup specifications (Section 6)
• Automated: Color palette validation script checks hex values match specification [TO BE CREATED]
• Green light: All 14 reference mockups match within perceptual similarity threshold; all 37 material categories render correctly

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1. Canonical Color Palette

All colors originate from the Virtual Worm February 2012 Blender model (Virtual_Worm_February_2012.blend), which defines 37 material categories covering the complete anatomy of C. elegans. These are the heritage colors — the closest thing the project has to a canonical palette, and they are preserved here.

1A. Heritage Palette — Virtual Worm 37 Materials

Extracted directly from Virtual_Worm_February_2012.mtl. RGB values are the Kd (diffuse) component. All materials share: specular exponent Ns=96, ambient Ka=(0,0,0), illumination model 2 (Blinn-Phong).

Muscle Tissues (7 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Body Wall Muscle	Body_Wall_Muscle	0.16, 0.32, 0.00	41, 82, 0	#295200	Dark green
Vulval Muscle	Vulval_Muscle	0.48, 0.64, 0.32	122, 163, 82	#7AA352	Yellow-green
Uterine Muscle	Uterine_Muscle	0.48, 0.64, 0.00	122, 163, 0	#7AA300	Bright yellow-green
Stomatointestinal Muscle	Stomatoint_Muscle	0.00, 0.32, 0.00	0, 82, 0	#005200	Forest green
Sphincter & Anal Depressor Muscle	Sphnc_&_Anal_Dep_Musc	0.32, 0.48, 0.00	82, 122, 0	#527A00	Olive green
Even Pharyngeal Muscle	Even#PhMusc	0.64, 0.80, 0.48	163, 204, 122	#A3CC7A	Light green
Odd Pharyngeal Muscle	Odd#PhMuscle	0.16, 0.64, 0.00	41, 163, 0	#29A300	Bright green

Design rationale: All muscles share the green family. Body wall muscles are the darkest green (most prominent, needs contrast with other tissues). Pharyngeal muscles are lighter green to distinguish from BWM. This green baseline is important because the activity-state overlay (Section 1B) shifts muscles toward red when contracted — the green→red dynamic range is the primary visual indicator of muscle state.

Neuron Types (5 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Interneuron	Interneuron	0.80, 0.16, 0.00	204, 41, 0	#CC2900	Orange-red
Motor Neuron	Motor_Neuron	0.48, 0.32, 0.75	122, 82, 190	#7A52BE	Purple-blue
Sensory Neuron	SensoryNeuron	0.80, 0.32, 0.75	204, 82, 190	#CC52BE	Magenta-pink
Polymodal Neuron	PolymodalNeuron	0.77, 0.01, 0.01	196, 2, 2	#C40202	Deep red
Neuron (Unknown Function)	NeurUnkFunc	0.48, 0.00, 0.16	122, 0, 41	#7A0029	Burgundy

Design rationale: Neuron types use warm/saturated colors that stand out against the green muscle background. Each functional class has a distinct hue to support visual identification. The activity-state overlay (Section 1B) modulates brightness, not hue — the base color always communicates neuron class.

Structural & Epithelial Tissues (14 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Hypodermis	Hypodermis	0.69, 0.61, 0.54	176, 156, 138	#B09C8A	Tan/beige
Seam Cell	Seam_Cell	0.64, 0.32, 0.16	163, 82, 41	#A35229	Brown
Intestine	Intestine	0.80, 0.64, 0.80	204, 163, 204	#CCA3CC	Light lavender
Pharyngeal Epithelium	Pharyngeal_Epithelium	0.48, 0.32, 0.32	122, 82, 82	#7A5252	Muted rose
Rectal Epithelium	Rectal_epithelium	0.48, 0.32, 0.32	122, 82, 82	#7A5252	Muted rose
Vulva Epithelium	Vulva_epithelium	0.48, 0.48, 0.80	122, 122, 204	#7A7ACC	Periwinkle
Arcade Cells	Arcade_Cells	0.64, 0.64, 0.00	163, 163, 0	#A3A300	Dark yellow
Socket Cell	SocketCell	0.80, 0.48, 0.48	204, 122, 122	#CC7A7A	Salmon
GLR Cells	GLR_Cells	0.75, 0.48, 0.00	190, 122, 0	#BE7A00	Amber
Marginal Cells	marginal_cells	0.75, 0.16, 0.75	190, 41, 190	#BE29BE	Magenta
Head Mesodermal Cell	Head_Mesodermal_Cell	0.80, 0.32, 0.16	204, 82, 41	#CC5229	Burnt orange
Coelomocyte	Coelomocyte	0.80, 0.64, 0.00	204, 163, 0	#CCA300	Gold
Pharyngeal & Rectal Glands	Phary_&_Rect_Glands	0.64, 0.64, 0.80	163, 163, 204	#A3A3CC	Lavender-gray
VPI & VIR	VPI_&_VIR	0.48, 0.32, 0.16	122, 82, 41	#7A5229	Brown

Excretory System (4 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Excretory Cell	Excretory_Cell	0.64, 0.16, 0.32	163, 41, 82	#A32952	Rose
Excretory Pore Cell	Excretory_Pore_Cell	0.74, 0.77, 0.45	189, 198, 114	#BDC672	Khaki
Excretory Duct Cell	Excretory_Duct_Cell	0.64, 0.48, 0.32	163, 122, 82	#A37A52	Tan
Excretory Gland Cells	Excretory_Gland_Cells	0.48, 0.48, 0.64	122, 122, 163	#7A7AA3	Steel blue

Reproductive System (5 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Germline	Germline	0.00, 0.16, 0.32	0, 41, 82	#002952	Dark navy
DTC & Somatic Gonad	DTC_&_Somatic_Gonad	0.48, 0.32, 0.80	122, 82, 204	#7A52CC	Purple
Spermatheca	Spermatheca	0.16, 0.48, 0.80	41, 122, 204	#297ACC	Blue
Spermathecal-Uterine Valve	Spermath_Uterin_Valve	0.32, 0.32, 0.48	82, 82, 122	#52527A	Slate
Uterus	Uterus	0.48, 0.64, 0.64	122, 163, 163	#7AA3A3	Teal

Other (2 materials)

Material	MTL Name	RGB (0-1)	RGB (0-255)	Hex	Visual Description
Sheath (Other)	SheathOther	0.16, 0.48, 0.48	41, 122, 122	#297A7A	Dark teal
Temp DRG Color	Temp_DRG_Color	0.77, 0.16, 0.00	198, 42, 0	#C62A00	Orange-red

Global Material Properties (from MTL)

All 37 Virtual Worm materials share these base properties:

Property	MTL Key	Value	Meaning
Specular exponent	Ns	96.078431	Moderately sharp specular highlights
Ambient	Ka	(0, 0, 0)	No ambient contribution (lighting-dependent)
Specular	Ks	(0, 0, 0)*	No specular highlights for most tissues
Opacity	d	0.05	5% opaque (highly translucent)
Illumination model	illum	2	Blinn-Phong shading

*Exception: Coelomocyte has Ks=(0.5, 0.5, 0.5) — a slight wet/glossy look, biologically motivated by their scavenger function.

Note on opacity: The MTL file specifies d=0.05 (5% opaque) for all materials. This works in the original Blender model where all 37 tissue layers are composited together — each layer contributes a faint wash of color, and stacking them produces the complete worm. In the interactive viewer, opacity must be adjusted per-context (see Section 3 for scale-specific opacity values).

1B. Activity-State Dynamic Colors

These are overlays on the base heritage colors. They communicate time-varying simulation state. When a cell is at rest, it shows its base color from Section 1A. When active, the dynamic mapping modifies brightness, hue, or opacity.

Data Source	Visual Property Modified	Rest State	Active State	Colormap	Scale Range	DD Source
Neuron membrane voltage	Brightness + hue shift	Base color at 30% brightness	Base color at 100% brightness + white core glow	Blue tint (rest) → base color (threshold) → white core (peak)	-80 mV (rest) to +20 mV (peak depolarization)	DD001
Neuron intracellular [Ca²⁺]	Additive glow color	No glow (black additive)	Gold/yellow glow (#FFD700)	Black (0) → Gold (max) additive blend	0 to max_ca (per-neuron normalized)	DD001
Muscle activation	Hue shift (green→red)	Base green color (#295200)	Red (#CC2200)	RdYlGn_r (reversed Red-Yellow-Green)	0.0 (relaxed) to 1.0 (max contraction)	DD002
Intestinal [Ca²⁺] per cell	Cell face color gradient	Cool blue (#2244CC)	Hot red (#CC2200)	Blue→Red (sequential)	0 to max_intestinal_ca	DD009
Pharynx pumping state	Opacity modulation	40% opacity (relaxed)	95% opacity (contracted)	Transparent→Opaque	0.0 (relaxed) to 1.0 (contracted)	DD007
Neuropeptide concentration	Volumetric cloud density + color	Fully transparent	Colored semi-transparent cloud	Per-peptide color, alpha ∝ concentration	0 to max_conc	DD006
SPH particle type	Point color (categorical)	N/A	N/A	Blue=liquid, Green=elastic, Gray=boundary	Categorical	DD003
Cell identity (DD004)	Cell outline color	Per-tissue-type color from 1A	N/A	Categorical (same as heritage palette)	Categorical	DD004

Voltage-to-Visual Mapping (Detail)

The neuron voltage mapping is the most visually complex dynamic overlay. Here is the precise algorithm:

input:  V (membrane voltage in mV), base_color (RGB from Section 1A)
output: rendered_color (RGB), glow_intensity (float 0-1)

V_rest   = -80.0   # mV
V_thresh = -40.0   # mV (approximate action potential threshold)
V_peak   = +20.0   # mV

# Normalize voltage to 0-1 range
t = clamp((V - V_rest) / (V_peak - V_rest), 0.0, 1.0)

# Brightness: ramp from 0.3 (rest) to 1.0 (peak)
brightness = 0.3 + 0.7 * t

# At rest (t < 0.25): tint toward blue
# At threshold (t ≈ 0.5): show base color at full brightness
# At peak (t > 0.85): blend toward white
if t < 0.25:
    blue_tint = RGB(0.2, 0.3, 0.6)
    rendered_color = lerp(blue_tint, base_color, t / 0.25) * brightness
elif t < 0.85:
    rendered_color = base_color * brightness
else:
    white = RGB(1.0, 1.0, 1.0)
    rendered_color = lerp(base_color, white, (t - 0.85) / 0.15) * brightness

# Glow: only emits above threshold
glow_intensity = max(0.0, (t - 0.5) / 0.5)  # 0 below threshold, ramps to 1.0

Muscle Activation Mapping (Detail)

input:  activation (float 0-1), base_green = RGB(0.16, 0.32, 0.0)
output: rendered_color (RGB)

relaxed_color   = RGB(0.16, 0.50, 0.0)   # Slightly brighter green than base
mid_color       = RGB(0.80, 0.80, 0.0)   # Yellow at half activation
contracted_color = RGB(0.80, 0.13, 0.0)  # Red at full contraction

if activation < 0.5:
    rendered_color = lerp(relaxed_color, mid_color, activation / 0.5)
else:
    rendered_color = lerp(mid_color, contracted_color, (activation - 0.5) / 0.5)

1C. Molecular-Scale Palette

These colors apply only at the molecular scale (Section 3C). They are new assignments (not from Virtual Worm) designed for visual clarity when viewing membrane cross-sections and intracellular dynamics.

Element	Hex	RGB (0-255)	Visual Description	Rationale
Na⁺ ion channel	#4488FF	68, 136, 255	Bright blue	Convention: Na⁺ = blue in electrophysiology diagrams
K⁺ ion channel	#44BB44	68, 187, 68	Green	Convention: K⁺ = green
Ca²⁺ ion channel	#FFD700	255, 215, 0	Gold	Matches calcium glow from 1B
Cl⁻ ion channel	#DD4444	221, 68, 68	Red	Convention: Cl⁻ = red
Lipid bilayer	#C8B8A8	200, 184, 168	Warm gray	Neutral background, slight biological warmth
IP3 receptor	#CC44CC	204, 68, 204	Magenta	Distinct from ion channels, signals second-messenger pathway
GPCR receptor	#44BBBB	68, 187, 187	Teal	Distinct from IP3, signals peptide reception
Ca²⁺ free ion	#FFD700	255, 215, 0	Gold (glowing)	Same as channel — continuity as Ca²⁺ flows through pore
Neuropeptide molecule	Per-peptide	Varies	Matches volumetric cloud color from 1B	Visual continuity across scales
Cell interior background	#0A0A14	10, 10, 20	Near-black with blue tint	Dark interior, slight cool tone suggests aqueous cytoplasm
Nucleus & Gene Expression
Nuclear envelope	#3D3570	61, 53, 112	Deep indigo	Double membrane, distinct from plasma membrane and ER
Nuclear pore complex	#6B5DAA	107, 93, 170	Medium purple	Lighter than envelope to show pore structure
Chromatin (inactive)	#1A1440	26, 20, 64	Very dark purple	Tightly packed, barely visible against nucleus interior
Chromatin (active locus)	#8877CC	136, 119, 204	Bright lavender	Glowing, unwound region where transcription is happening
RNA polymerase II	#FF8844	255, 136, 68	Bright orange	Warm, highly visible — the "engine" of transcription
mRNA transcript	#FF6688	255, 102, 136	Coral pink	Warm pink strand, visually tracks from nucleus → cytoplasm
Nuclear pore transit glow	#AA88FF	170, 136, 255	Soft violet	Brief glow when mRNA passes through nuclear pore
Ribosome	#66AA66	102, 170, 102	Muted green	Distinct from ion channels; biological convention (green for translation)
Rough ER membrane	#8A7A6A	138, 122, 106	Warm dark gray	Same as smooth ER, but studded with green ribosome dots
Nascent protein (folding)	#DDBB44	221, 187, 68	Warm gold-yellow	Emerging from ribosome, color hints at final channel identity
Transport vesicle	#55AADD	85, 170, 221	Sky blue	Distinct from all other elements; suggests fluid transport
Vesicle membrane fusion glow	#88DDFF	136, 221, 255	Bright cyan	Flash when vesicle fuses with plasma membrane

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2. Lighting & Environment

2A. Global Lighting Setup

All scales share a three-point lighting rig, with parameters adjusted per scale.

Light	Type	Position (relative to camera)	Color	Intensity	Purpose
Key light	Directional	30° above, 45° right	#FFFAF0 (warm white)	1.0	Primary illumination, defines form
Fill light	Directional	15° above, 30° left	#E8E8FF (cool white)	0.4	Softens shadows, prevents pure-black regions
Rim light	Directional	10° above, directly behind	#FFFFFF (pure white)	0.6	Silhouette separation from background

2B. Background

Scale	Background	Specification
Organism	Dark gradient	Linear gradient from #1A1A2E (top) to #16213E (bottom). No environment map, no grid, no distracting elements. The worm is the sole subject.
Tissue/Cell	Same dark gradient	Consistent with organism scale; depth-of-field blur softens background cells.
Molecular	Cell interior	#0A0A14 (near-black). Slight procedural noise texture (amplitude 0.02, frequency 0.5/µm) to suggest cytoplasmic structure without distracting from channels.

2C. Material Model

Property	WebGPU (Three.js Phase 2/3)	WebGL Fallback (Phase 1 / Trame)
Shading model	PBR (MeshStandardMaterial)	Phong (MeshPhongMaterial)
Metalness	0.0 (all biological tissues)	N/A (Phong has no metalness)
Roughness	0.6 (default for soft tissue)	Shininess = 30 (approximate equivalent)
Roughness: cuticle	0.3 (smoother, slightly glossy)	Shininess = 60
Roughness: wet tissue (intestine, gonad)	0.4 (slightly glossy)	Shininess = 45
Subsurface scattering	Enabled for cuticle (WebGPU only)	Not available — use alpha=0.85 + backface coloring as approximation
Normal maps	Used for muscle striations (tissue scale)	Same
Emissive	Used for active neurons (glow_intensity from 1B)	Same (emissive color = base_color * glow_intensity)

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3. Scale-Specific Rendering Specifications

3A. Organism Scale

What the user sees: A smooth, translucent C. elegans body crawling. Body bends propagate as sinusoidal waves. The pharynx is faintly visible through the cuticle as a rhythmic shadow. Defecation contractions are visible as a brief posterior-to-anterior tightening.

Surface

Property	Value	Notes
Geometry source	Marching cubes isosurface from SPH particles (Phase 1); VirtualWorm mesh skinning (Phase 2+)	See DD014 Surface Reconstruction
Cuticle opacity	0.85	Semi-translucent — internal structures visible as shadows
Cuticle color	#B09C8A (Hypodermis) with slight desaturation	The outermost visible surface uses the hypodermis color
Cuticle roughness	0.3	Smoother than internal tissues — worm cuticle has a slight sheen
Subsurface scattering radius	0.15 mm (WebGPU)	Light penetrates thin cuticle, creating soft internal glow
Surface normal smoothing	Laplacian smooth, 2 iterations	Removes marching-cubes staircase artifacts
Body bend visualization	Surface deformation from SPH particle motion	No artificial displacement — the physics engine drives the shape
Muscle ridges (Phase 2+)	Subtle normal-map perturbation on dorsal/ventral muscle quadrants	Amplitude 0.02 mm, 24 ridges per quadrant matching BWM count

Internal Visibility Through Cuticle

When the body surface layer is ON (default), internal structures are visible only as shadows and color wash through the translucent cuticle:

• Pharynx pumping: Appears as a rhythmic darkening/lightening at the anterior, ~3-4 Hz
• Intestine: Faint lavender (#CCA3CC) wash visible through mid-body
• Muscles: Not individually visible — their effect is seen as body bending

To see individual cells, the user must zoom to tissue scale or toggle body surface OFF.

Camera

Property	Value
Default position	Dorsal view, camera 800 µm from body center
Field of view	35° (tight framing, worm fills ~70% of viewport width)
Orbit	Free orbit (trackball rotation), clamped to prevent camera-inside-body
Pan	Right-click drag or two-finger drag
Zoom	Scroll wheel, continuous (triggers scale transition at breakpoints)

3B. Tissue / Cell Scale

What the user sees: Individual cells as distinct colored shapes. Muscles show green→red activation. Neurons glow when depolarized. Cell boundaries are visible as thin outlines. Clicking any cell opens the inspector panel.

Zoom breakpoint: Tissue scale activates when camera distance < 400 µm from nearest body surface point.

Cell Geometry

Property	Value	Notes
Cell shape source	VirtualWorm OBJ meshes (per-tissue groupings)	Each tissue type is a separate mesh in the OBJ
Individual cell segmentation	DD004 particle-to-cell mapping → convex hull per cell (Phase 2+)	Phase 1 uses tissue-level meshes, not individual cells
Cell boundary outlines	1.5 px screen-space line in 30%-darkened base color	E.g., Body Wall Muscle outline = #1D3600 (darker #295200)
Cell boundary visibility	OFF by default; toggled via "Cell boundaries" layer	Reduces visual clutter at default view

Neuron Rendering

Property	Value	Notes
Soma geometry	Sphere, radius from NeuroML morphology (typically 2-4 µm)	Loaded from .cell.nml files via Worm3DViewer's neuromlmodel.py
Dendrite/axon geometry	Cylindrical tubes following NeuroML segment coordinates	Radius from NeuroML; minimum 0.3 µm for visibility
Base color	From Section 1A neuron type table	Interneuron=#CC2900, Motor=#7A52BE, etc.
Resting appearance	Base color at 30% brightness, no glow	Neuron is present but visually quiet
Active appearance	Full brightness + bloom glow	See voltage mapping in Section 1B
Bloom post-process	Gaussian blur, kernel 9px, threshold = 0.7 × max emissive intensity	Only active neurons emit enough to exceed bloom threshold
Bloom color	Matches base color (not white)	Interneuron glow is orange-red, motor neuron glow is purple
Selected neuron highlight	White wireframe overlay + inspector panel open	2px white wireframe on soma + connected segments

Muscle Rendering

Property	Value	Notes
Geometry	VirtualWorm bwm.obj mesh faces, grouped by muscle ID	95 muscles in 4 quadrants
Base color (relaxed)	#295200 (Body Wall Muscle)	From Section 1A
Activated color	Green→Yellow→Red per Section 1B	RdYlGn_r colormap
Striations (Phase 2+)	Normal map: parallel ridges along muscle long axis	Period 2 µm, amplitude 0.01 mm, visible only at close zoom
Opacity	0.9	Nearly opaque when muscle layer is ON

Pharynx Detail View

Visible when zoomed into anterior region and pharynx layer is ON.

Property	Value	Notes
Cell geometry	63 cells from VirtualWorm pharyngeal meshes	Includes pm1-pm8 muscles, mc1-mc3 marginal cells, epithelial cells
Pumping animation	Opacity modulation per-section (corpus / isthmus / terminal bulb)	See Section 1B: 40% relaxed → 95% contracted
Pumping frequency	3-4 Hz (from DD007 simulation output)	Visual should match this rate
Grinder visualization (Phase 3)	Rotation animation of terminal bulb interior	Simplified: sinusoidal rotation ±15° synchronized with pump cycle
Pharyngeal neuron visibility	20 pharyngeal neurons visible when neurons layer ON	Colors from Section 1A by neuron type

Intestinal Calcium Wave

Visible when intestine layer is ON.

Property	Value	Notes
Cell geometry	20 int cells, tube arrangement (from VirtualWorm Intestine mesh segments)	Each cell is a ring-segment of the tube
Resting color	Blue (#2244CC)	Cool blue = low [Ca²⁺]
Peak calcium color	Red (#CC2200)	Hot red = high [Ca²⁺]
Wave propagation	Posterior→anterior color gradient, each cell transitions blue→red→blue	One wave every ~50 seconds (DD009 defecation motor program period)
Transition speed per cell	~2 seconds rise, ~5 seconds fall	Matches biological IP3-mediated calcium dynamics

Depth of Field

Property	Value
Focus point	Center of currently selected cell, or screen center
Focal distance	Camera-to-focus-point distance
Aperture (f-stop equivalent)	f/2.8 (shallow) at tissue scale; f/8 (deep) at organism scale
Bokeh shape	Circular
Implementation	Post-process CoC (circle of confusion) blur; WebGPU compute or fragment shader

3C. Molecular Scale

What the user sees: A cross-section of a cell membrane with embedded ion channel proteins. Calcium ions flow through open channels as glowing gold particles. The lipid bilayer is a textured surface with protein complexes embedded in it.

Zoom breakpoint: Molecular scale activates when camera distance < 5 µm from a selected cell's membrane.

Membrane Cross-Section

Property	Value	Notes
Lipid bilayer geometry	Textured plane, 200nm × 200nm visible area, 7nm thick	Two parallel sheets with hydrophobic tails facing inward
Bilayer color	#C8B8A8 (warm gray)	From Section 1C
Bilayer texture	Procedural: packed ellipses (lipid heads) on surface, random orientation	Head diameter ~0.7nm, gap ~0.1nm
Bilayer opacity	0.7	Translucent enough to see channel pores through the membrane
Bilayer edge treatment	Fades to transparent at visible-area boundary	No sharp edge — membrane extends beyond view

Ion Channel Glyphs

Property	Value	Notes
Channel geometry	Simplified cylinder pore (outer diameter 8nm, pore diameter 0.5-2nm) embedded in bilayer	Not atomistic — schematic representation
Channel color	By ion selectivity (Section 1C): Na⁺=blue, K⁺=green, Ca²⁺=gold, Cl⁻=red
Channel material	Roughness 0.4, slight metalness 0.1	Protein has a faint sheen, distinguishes from lipid
Closed state	Pore diameter 0.5nm, channel color at 50% brightness	Visually "pinched shut"
Open state	Pore diameter 2nm, channel color at 100% brightness + subtle glow	Pore visibly dilated
Gating animation	Pore diameter interpolation over 200ms	Simplified conformational change
Channel density	From DD005 CeNGEN expression data mapped to conductance density	Approximate: 1-5 channels per 200nm² patch

Ion Particles

Property	Value	Notes
Ca²⁺ geometry	Sphere, visual radius 1nm (exaggerated ~5× for visibility)	Actual ionic radius is ~0.1nm — too small to see
Ca²⁺ color	#FFD700 (gold)	Matches channel and glow from Section 1B/1C
Ca²⁺ glow	Emissive material, intensity 0.8	Glowing spheres stand out against dark interior
Ca²⁺ motion	GPU particle system, physics-based diffusion + channel transit	When channel opens: ions flow through pore along concentration gradient
Flow speed through channel	50 nm/ms (exaggerated for visibility)	Real transit time is ~10ns — imperceptibly fast at real scale
Extracellular Ca²⁺	Sparse gold particles above membrane, random Brownian motion	Concentration: ~5 particles per 200nm² at 2mM extracellular
Intracellular Ca²⁺	Very sparse gold particles below membrane	~0-1 particles per 200nm² at 100nM resting; increases during influx

Neuropeptide Molecules (Molecular Scale)

Property	Value	Notes
Geometry	Icosphere, visual radius 3nm (exaggerated)	Peptides are larger than ions but still sub-microscopic
Color	Per-peptide (matches volumetric cloud from tissue scale)	Visual continuity across zoom levels
Glow	Emissive intensity 0.5	Less bright than Ca²⁺ — peptides are modulatory, not the main event
Motion	Brownian diffusion in extracellular space	Slower than ions; diffusion coefficient ~10⁻⁶ cm²/s
GPCR binding	Peptide snaps to receptor glyph, brief flash, then fades	500ms animation

Cell Interior & Nucleus

The molecular scale reveals not just the membrane but the entire intracellular scene — from the nucleus where ion channel genes are transcribed, through mRNA export and ribosomal translation on the rough ER, to vesicle trafficking that delivers newly synthesized channel proteins to the plasma membrane. This connects DD005 (CeNGEN gene expression data) directly to the functional channels visible at the membrane surface.

Scene layout (cross-section view, top to bottom):

    ═══════════════════════════════  Extracellular space (light)
    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  Plasma membrane (channels embedded)
    ░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░  Cytoplasm (dark, with vesicles in transit)
    ▓▓▓▓▓   Rough ER (ribosomes)   ▓▓▓  Smooth ER
    ░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░  Cytoplasm
    ╔══════════════════════════╗      Nuclear envelope (double membrane)
    ║  ●  Chromatin            ║      Nuclear pore complexes at gaps
    ║     ✦ Active locus       ║      RNA Pol II visible at active gene
    ║        ~ mRNA emerging   ║
    ╚══════════════════════════╝

Nucleus

Property	Value	Notes
Geometry	Ellipsoid, ~3 µm diameter (visual, scaled to cell type)	Positioned in lower half of cross-section view
Nuclear envelope	Double membrane, indigo (#3D3570), 30nm gap between membranes (exaggerated for visibility)	Slight translucency (opacity 0.8) so interior is visible
Nuclear pore complexes	8-sided ring structures (#6B5DAA), ~120nm diameter, spaced ~200nm apart on envelope	Visible as gaps/portals in the nuclear membrane
Nuclear interior	#0D0A20 (darker than cytoplasm, slightly purple-tinted)	Distinct from cytoplasm to show compartmentalization
Chromatin (bulk)	Dense, thread-like masses, very dark purple (#1A1440)	Procedural: Perlin-noise-displaced tubes, tightly packed, low opacity
Chromatin (active gene locus)	Bright lavender (#8877CC) unwound loop, emissive glow intensity 0.4	Only 1-3 active loci visible at a time; which genes are active depends on DD005 CeNGEN data for this cell type

Gene Transcription (at Active Locus)

This is the first stage of the gene expression pipeline. The user sees a gene being read and an mRNA strand emerging.

Property	Value	Notes
RNA Polymerase II	Sphere-cluster glyph (~15nm), bright orange (#FF8844), emissive 0.3	The "machine" crawling along the DNA. Visually prominent.
Pol II motion	Slides along active chromatin loop at ~50nm/s (exaggerated 1000× for visibility)	Real rate: ~25 nt/s ≈ 8nm/s. Sped up so the process is watchable.
Nascent mRNA	Coral pink (#FF6688) strand emerging from Pol II, growing in length	Rendered as a bezier-curve tube (radius 1nm visual), growing 1nm per frame from Pol II
mRNA completion	When strand reaches ~200nm visual length, it detaches from Pol II and coils slightly	Simplified: no splicing shown (intron removal happens but is not visually rendered to avoid clutter)
Active gene label	Floating text label near active locus: gene name (e.g., "egl-19 (Ca²⁺ channel)")	Font: 8px screen-space, #AAAAAA, fades at distance
Transcription frequency	Driven by DD005 CeNGEN expression level for this cell type	High-expression genes: new Pol II starts every ~5 seconds. Low-expression: every ~30 seconds.

Which genes are shown: At any time, 1-3 gene loci are visually active, selected from the ion channel / receptor genes that DD005 maps to this cell type. For a motor neuron, this might include unc-2 (Ca²⁺ channel), egl-36 (K⁺ channel), and unc-49 (GABA receptor). The viewer cycles through the cell's expressed channel genes over time.

mRNA Nuclear Export

Property	Value	Notes
mRNA travel to pore	Completed mRNA coils into a ~30nm ball, drifts toward nearest nuclear pore	Brownian-biased motion toward pore, ~100nm/s
Nuclear pore transit	mRNA ball passes through pore ring; pore ring briefly glows violet (#AA88FF) for 300ms	The "aha" moment — genetic information leaving the nucleus
Export animation	mRNA ball squeezes slightly as it passes through pore (scale X/Z to 0.7, then back to 1.0)	Communicates that the pore is a selective barrier
Post-export	mRNA enters cytoplasm, uncoils slightly into an elongated coil, drifts toward rough ER	Color remains coral pink (#FF6688) for visual tracking continuity

Ribosomal Translation (on Rough ER)

Property	Value	Notes
Rough ER geometry	Folded membrane sheets, warm dark gray (#8A7A6A), positioned between nucleus and plasma membrane	~5nm thick membrane with visible ribosomes studded on cytoplasmic face
Ribosome geometry	Small sphere doublet (~25nm, large + small subunit), muted green (#66AA66)	Packed along ER surface, ~30nm spacing
mRNA docking	mRNA strand threads through a ribosome; ribosome begins glowing slightly (emissive 0.2)	Contact triggers the translation animation
Translation animation	Ribosome slides along mRNA at ~20nm/s; a warm gold-yellow (#DDBB44) nascent protein strand emerges on the ER-lumen side	The protein is being synthesized and simultaneously inserted into the ER membrane
Nascent channel protein	Gold-yellow strand folds into a simplified cylinder shape as it grows	Folding: tube collapses into a compact form over ~3 seconds
Completion	Ribosome releases mRNA, falls off; completed channel protein is now embedded in ER membrane	Protein takes on its final ion-channel color (e.g., gold for Ca²⁺, blue for Na⁺)

Vesicle Trafficking (ER → Plasma Membrane)

Property	Value	Notes
Vesicle budding	A bump forms on the ER membrane, pinches off as a sphere (~50nm visual radius), sky blue (#55AADD)	The channel protein is visible as a colored dot embedded in the vesicle membrane
Vesicle motion	Vesicle drifts from ER toward plasma membrane along a slightly curved path	~200nm/s (exaggerated). In reality, motor proteins carry vesicles along microtubules — simplified to smooth drift.
Vesicle contents	1-2 channel proteins visible as colored patches on vesicle surface	E.g., a gold dot for a Ca²⁺ channel being delivered
Membrane fusion	Vesicle contacts plasma membrane → brief bright cyan flash (#88DDFF, 200ms) → vesicle membrane merges with plasma membrane	The channel protein is now in the plasma membrane and functional
Post-fusion	New channel appears at fusion site in closed state	Connects the gene expression pipeline to the existing channel gating visualization

Gene Expression Pipeline — Complete Visual Narrative

The full sequence a user can watch at molecular scale:

1. NUCLEUS: Chromatin locus glows → RNA Pol II transcribes gene → mRNA strand grows
2. EXPORT:  mRNA coils → drifts to nuclear pore → squeezes through (violet flash)
3. TRANSIT: mRNA drifts through cytoplasm to rough ER
4. TRANSLATION: mRNA docks at ribosome → ribosome slides along → protein strand emerges
5. FOLDING: Nascent protein folds into channel shape, takes on ion-type color
6. TRAFFICKING: Vesicle buds from ER with embedded channel → drifts to plasma membrane
7. INSERTION: Vesicle fuses (cyan flash) → new channel appears in membrane, closed state
8. FUNCTION: Channel responds to voltage/ligand → opens → ions flow through

Total pipeline duration (visual, exaggerated): ~30-60 seconds per channel protein. Real biological timescale: minutes to hours. The exaggeration makes the process watchable in a single viewing session.

Data source: The rate and type of channels being produced is driven by DD005 CeNGEN expression levels for the selected cell. A cell with high egl-19 expression produces Ca²⁺ channels more frequently than a cell with low expression.

Existing Intracellular Elements (Updated Context)

Property	Value	Notes
Cytoplasm background	#0A0A14 with noise texture	Dark, aqueous feel
IP3 receptor (on ER membrane)	Magenta (#CC44CC) cylinder, on ER lumen-facing surface	Visually distinct from plasma membrane channels; connects to DD009 intestinal Ca wave
Smooth ER membrane	Warm gray (#8A7A6A), continuous with rough ER but no ribosomes	Positioned near nucleus; IP3 receptors are here
Rough ER membrane	Same gray, but studded with green ribosome spheres	Between nucleus and plasma membrane; translation happens here
Ca²⁺ release from ER	Gold particles emerge from IP3 receptor when activated	Connects to DD009 intestinal calcium wave at molecular level
Microtubule hints (Phase 3)	Faint gray lines (#333340) from nucleus toward cell periphery	Not individually modeled; subtle visual guides suggesting cytoskeletal structure. Vesicles follow these paths.

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4. Multi-Scale Transitions

4A. Zoom Breakpoints

Scale transitions are triggered by camera distance to the nearest object. Three discrete scales with smooth transitions between them:

Transition	Camera Distance Trigger	Duration	Direction
Organism → Tissue	< 400 µm from body surface	0.75 seconds	Zoom in
Tissue → Organism	> 500 µm from body surface	0.75 seconds	Zoom out
Tissue → Molecular	< 5 µm from selected cell membrane	1.0 seconds	Zoom in (requires cell selection)
Molecular → Tissue	> 8 µm from membrane	1.0 seconds	Zoom out

Hysteresis gap (e.g., 400 µm in, 500 µm out) prevents flickering at boundary.

4B. Organism → Tissue Transition

Animated sequence (0.75 seconds):

Time (normalized)	Body Surface	Cells	Neurons/Muscles
0.0 (organism)	Opacity 0.85, smooth surface	Hidden	Hidden
0.0-0.3	Opacity fades 0.85 → 0.3	Begin fading in from 0% opacity	Begin fading in
0.3-0.7	Surface becomes wireframe (edges only, 1px white, opacity 0.2)	Opacity rises to 0.7	Individual neurons/muscles appear at base brightness
0.7-1.0	Wireframe fades to invisible	Full opacity (per-layer settings)	Fully visible with activity coloring

4C. Tissue → Molecular Transition

Requires a cell to be selected (clicked) before zoom can proceed to molecular scale.

Animated sequence (1.0 seconds):

Time (normalized)	Surrounding Cells	Selected Cell	Membrane/Channels
0.0 (tissue)	Visible, activity-colored	Highlighted (white wireframe)	Hidden
0.0-0.3	Fade to 10% opacity	Camera orbits to face cell membrane	Hidden
0.3-0.6	Hidden	Cell surface becomes translucent, cross-section plane appears	Lipid bilayer materializes along cross-section plane
0.6-1.0	Hidden	Cell surface fades out	Channels, ions, receptors appear; particle system starts

4D. Level of Detail (LOD)

To maintain 60fps during transitions and at tissue scale with 959 cells visible:

LOD Level	Camera Distance	Geometry	Shading
LOD 0 (full)	< 50 µm	Full mesh from VirtualWorm/NeuroML	Full PBR/Phong + activity coloring + bloom
LOD 1 (medium)	50-200 µm	Simplified mesh (50% triangle reduction)	Full shading, no bloom
LOD 2 (low)	200-500 µm	Convex hull per cell	Flat shading (base color only, no lighting calc)
LOD 3 (billboard)	> 500 µm	Camera-facing quad (sprite)	Solid color dot, size ∝ 1/distance

LOD transitions use alpha-blended cross-fade over 5 frames to prevent popping.

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5. Rendering Technique Specifications

5A. Transparency

The viewer composites multiple semi-transparent layers (cuticle, muscles, neurons, neuropeptide clouds). Naive alpha blending produces order-dependent artifacts.

Technique	When Used	Specification
Order-Independent Transparency (OIT)	WebGPU path (Phase 2/3)	Weighted Blended OIT (McGuire & Bavoil 2013). Weight function: w = alpha * max(0.01, min(3000, 10 / (0.00001 + pow(z/200, 4)))) where z is view-space depth.
Depth-sorted alpha blending	WebGL/Trame fallback (Phase 1)	Sort transparent objects back-to-front per frame. Acceptable for < 100 transparent objects.
Dual-depth peeling	Volumetric neuropeptide clouds	For high-quality volumetric compositing when OIT is insufficient.

5B. Bloom / Glow Post-Processing

Active neurons emit light (emissive material). Bloom creates the "glow" effect.

Parameter	Value	Notes
Bloom threshold	0.7 × max emissive intensity	Only neurons above ~-40mV threshold produce bloom
Bloom passes	5 (progressive downsample/upsample)	Standard Kawase or dual-filter blur
Bloom kernel size	9px at full resolution	Expands with each downsample pass
Bloom intensity	0.4	Subtle halo, not overwhelming
Bloom color	Source emissive color (not white)	Interneuron bloom is orange, motor neuron bloom is purple

5C. Particle Rendering

Used for SPH body particles (organism scale, scientific view), calcium ions (molecular scale), and neuropeptide molecules.

Property	SPH Particles	Ca²⁺ Ions	Neuropeptide Molecules
Count	~100,000	10-200 (per visible patch)	5-50 (per visible region)
Technique	GPU instanced rendering (InstancedMesh)	GPU instanced spheres	GPU instanced icospheres
Size	2 µm (screen-space minimum 1px)	1 nm visual radius (screen-space minimum 2px)	3 nm visual radius
Color source	Particle type (Blue/Green/Gray)	#FFD700 gold, emissive	Per-peptide from Section 1C
Billboard	No (true spheres at close range, points at distance)	Yes (always face camera)	No (rotation visible)
Motion update	Per-frame from Zarr time series	Physics-based particle system (GPU compute)	Brownian diffusion (GPU compute)

5D. Volumetric Rendering (Neuropeptide Clouds)

Neuropeptide concentration fields (DD006) are rendered as semi-transparent volumetric clouds at tissue scale.

Property	Value	Notes
Algorithm	Ray marching through 3D concentration texture	Fragment shader; one ray per pixel
Volume data	3D texture from DD006 concentration field, resampled to 64³ voxels per visible region	Updated per animation frame from Zarr
Step size	voxel_size / 2	Nyquist sampling to avoid aliasing
Max steps	128	Performance cap; early-exit when accumulated alpha > 0.95
Transfer function	Alpha = concentration / max_conc × 0.3 (max cloud opacity 30%)	Faint overlay, never obscures underlying cells
Color	Per-peptide assignment; if no specific assignment, default to #8844AA (purple mist)	Each neuropeptide family gets a unique hue
Blending	Additive (front-to-back accumulation with premultiplied alpha)	Overlapping peptide fields combine additively

5E. Anti-Aliasing

Technique	When Used
MSAA 4×	Default for all rendering paths
FXAA (post-process)	Fallback when MSAA unavailable or too expensive
Temporal AA	WebGPU path (Phase 3) for smoother animation

5F. Animation & Performance

Property	Target	Notes
Frame rate	60 fps	On 2020-era laptop with discrete GPU
Minimum acceptable	15 fps	On 2020-era laptop with integrated GPU (per DD014 QC5)
Simulation timestep interpolation	Linear interpolation between adjacent Zarr timesteps	Prevents jerky playback when Zarr export interval > 1
Playback speed	Configurable 0.1× to 10× real-time	Default: 1×
Time scrubbing	Instant seek to any timestep (load from Zarr chunk)	Progressive: show cached low-res first, then full resolution

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6. Reference Mockup Specifications

These 14 views define "correct" rendering. Each is described with enough detail to unambiguously determine whether an implementation screenshot matches. Mockups 1-12 cover organism, tissue, and membrane scales; Mockups 13-14 cover intracellular/nuclear gene expression.

Mockup 1: Organism — Dorsal View (Crawling)

Property	Specification
Camera	Dorsal (looking down onto worm's back), distance 800 µm
Visible layers	Body surface (ON), others OFF
Time point	Mid-crawl (body showing 1.5 sinusoidal bends)
Body	Smooth cuticle surface, #B09C8A with slight translucency
Background	#1A1A2E → #16213E gradient
Expected visual	A recognizable worm shape, ~1mm long, S-curved mid-crawl. Smooth surface with slight sheen. Faint internal shadows visible. Anterior (pharynx) at left, posterior at right.

Mockup 2: Organism — Lateral View (Body Bending)

Property	Specification
Camera	Lateral (side view), distance 800 µm, 10° above horizontal
Visible layers	Body surface (ON)
Time point	Same as Mockup 1
Expected visual	Worm body seen from the side. Dorsal-ventral thickness visible (~80 µm). Sinusoidal bending in the dorsal-ventral plane. Rim light creates bright edge along dorsal surface.

Mockup 3: Muscles Through Translucent Body

Property	Specification
Camera	Lateral view, distance 500 µm
Visible layers	Body surface (ON, opacity 0.5 — reduced for this view), Muscles (ON)
Time point	Mid-crawl with clear dorsal-ventral alternation
Expected visual	Semi-transparent cuticle revealing 4 quadrants of body wall muscles. Dorsal muscles are red (contracted) where body bends dorsally; corresponding ventral muscles are green (relaxed). Pattern alternates along body length.

Mockup 4: Neural Circuit Overview

Property	Specification
Camera	Dorsal view, distance 600 µm
Visible layers	Body surface (OFF), Neurons (ON)
Time point	Mid-activity (locomotion command active)
Expected visual	302 neurons visible as colored spheres with dendrite/axon tubes. Most neurons dim (resting). Command interneurons (AVA, AVB at anterior) glowing bright orange-red. Motor neurons along ventral cord showing alternating activation pattern (purple glow propagating). Sensory neurons in head region faint magenta. Clear distinction between neuron classes by color.

Mockup 5: Single Neuron Selected (Inspector Panel)

Property	Specification
Camera	Oblique anterior view, distance 200 µm, centered on AVAL
Visible layers	Neurons (ON), Muscles (ON at 30% opacity)
Time point	AVAL at peak depolarization
Selected	AVAL neuron — white wireframe highlight
Inspector panel	Visible at right side. Shows: "AVAL", "Command Interneuron", voltage trace (line plot, 2 seconds of history), calcium trace, list of synaptic partners.
Expected visual	AVAL soma glowing bright orange-red with bloom halo. Surrounding neurons at various activity levels. Inspector panel with live data.

Mockup 6: Pharynx Close-Up (Pumping)

Property	Specification
Camera	Anterior, distance 100 µm, facing into pharynx
Visible layers	Body surface (OFF), Pharynx (ON), Neurons (ON at 50% opacity)
Time point	Mid-pump (corpus contracted, isthmus relaxed, terminal bulb relaxing)
Expected visual	63 pharyngeal cells visible. Corpus region opaque (contracted, green muscles bright). Isthmus translucent (relaxed). Terminal bulb semi-opaque. Pharyngeal neurons (M1-M5, MC) visible as small glowing points among the muscle cells.

Mockup 7: Intestinal Calcium Wave (Mid-Propagation)

Property	Specification
Camera	Lateral view, distance 300 µm, centered on mid-body
Visible layers	Body surface (OFF), Intestine (ON)
Time point	Calcium wave at ~40% propagation (cells 8-12 of 20 at peak)
Expected visual	20 intestinal cells as tube segments. Posterior cells (1-7) returning to blue (wave has passed). Cells 8-12 bright red (peak calcium). Cells 13-20 still blue (wave hasn't arrived). Clear gradient visible at wave front.

Mockup 8: Neuropeptide Volumetric Cloud Overlay

Property	Specification
Camera	Dorsal view, distance 500 µm
Visible layers	Neurons (ON), Neuropeptides (ON)
Time point	Active neuromodulatory state (e.g., serotonergic neurons releasing peptides)
Expected visual	Neural circuit visible as in Mockup 4. Additionally, faint colored clouds surround releasing neurons — semi-transparent volumes that extend beyond the neuron soma, indicating diffusion range. Clouds are colored per peptide type. Multiple overlapping clouds visible with additive blending.

Mockup 9: Cell Boundaries (DD004 Tagging)

Property	Specification
Camera	Lateral view, distance 200 µm, focused on mid-body region
Visible layers	Body surface (OFF), Cell boundaries (ON), Muscles (ON at 50% opacity)
Time point	Any (static property)
Expected visual	Individual cell outlines visible as thin dark lines. Each cell filled with its tissue-type color. Muscle cells green, hypodermal cells tan, seam cells brown. Cell boundaries clearly delineate individual cells — not tissue-level blobs.

Mockup 10: Molecular — Membrane Cross-Section with Channels

Property	Specification
Camera	Perpendicular to membrane surface, distance 100 nm
Visible layers	Molecular (ON) — automatically active at this zoom
Time point	Resting state (channels mostly closed)
Expected visual	Lipid bilayer as warm gray textured surface spanning the viewport. 3-5 ion channel proteins embedded: gold (Ca²⁺), blue (Na⁺), green (K⁺) cylinders with visible closed pores. Dark cell interior below, lighter extracellular space above. A few scattered gold Ca²⁺ ions in extracellular space.

Mockup 11: Molecular — Calcium Flowing Through Open Channel

Property	Specification
Camera	Side view of membrane, distance 50 nm, angled 30° from membrane normal
Visible layers	Molecular (ON)
Time point	Ca²⁺ channel open, active influx
Expected visual	One Ca²⁺ channel (gold) in center, pore visibly open (dilated). Stream of gold glowing spheres (Ca²⁺ ions) flowing through the pore from extracellular (top) to intracellular (bottom). Ions above membrane: sparse, random. Ions in channel: aligned, fast-moving. Ions below membrane: dispersing into cell interior. Channel glowing brighter than neighbors (which are closed).

Mockup 12: Multi-Scale Transition (Organism → Tissue, Mid-Zoom)

Property	Specification
Camera	Lateral view, distance 400 µm (at transition breakpoint)
Visible layers	Body surface (mid-fade), Muscles (appearing), Neurons (appearing)
Time point	Mid-crawl
Expected visual	Body surface at reduced opacity (~0.4), partially wireframe. Individual muscle cells beginning to appear as green/red shapes beneath the fading cuticle. Some neurons visible as faint colored spheres. A "between-worlds" view showing both the smooth organism and the cellular interior simultaneously.

Mockup 13: Molecular — Nucleus and Gene Transcription

Property	Specification
Camera	Interior view, distance 2 µm from nucleus center, looking at nuclear surface
Visible layers	Molecular (ON) — zoomed past membrane into cell interior
Time point	Active transcription of egl-19 (Ca²⁺ channel gene)
Expected visual	Indigo nuclear envelope fills the lower half of the frame, with 3-4 nuclear pore complexes visible as purple ring structures. Through the translucent envelope, dark chromatin masses are visible inside. One locus glows bright lavender — the active gene. A bright orange RNA Polymerase II complex sits on the unwound chromatin. A coral pink mRNA strand extends from the polymerase, growing visibly. A gene label ("egl-19 (Ca²⁺ channel)") floats near the locus. In the upper portion of the frame, rough ER membranes with green ribosome dots are faintly visible.

Mockup 14: Molecular — mRNA Export and Channel Assembly

Property	Specification
Camera	Side view showing nucleus (left), cytoplasm (center), plasma membrane (right), distance 3 µm — wide enough to see the full pipeline
Visible layers	Molecular (ON)
Time point	Multiple pipeline stages simultaneously visible
Expected visual	Left: Nuclear envelope with one pore glowing violet as an mRNA ball squeezes through it. Center-left: A completed coral pink mRNA coil drifting toward rough ER. Center: A ribosome on the ER glowing faintly, with a gold-yellow nascent protein strand emerging through the ER membrane — a channel protein being built. Center-right: A sky blue transport vesicle with a gold dot (Ca²⁺ channel) embedded in it, drifting toward the plasma membrane. Right: The plasma membrane with existing channels; a cyan flash where a vesicle just fused, depositing a new channel. The entire gene-to-channel pipeline is visible in a single frame — from transcription to functional membrane protein.

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7. Assigning Colors to All 959 Cells

The Virtual Worm palette defines 37 material categories, not 959 individual cell colors. Every cell in C. elegans maps to one of these categories based on its tissue type. The mapping uses WormBase cell ontology (WBbt) identifiers and is resolved by DD004 (Mechanical Cell Identity) and DD008 (Data Integration Pipeline).

Cell-to-Material Mapping Rules

Cell Class	Count	Material Category	Base Color
Body wall muscle cells	95	Body_Wall_Muscle	#295200
Pharyngeal muscle cells (pm1, pm3, pm5, pm7)	~20	Odd#PhMuscle	#29A300
Pharyngeal muscle cells (pm2, pm4, pm6, pm8)	~20	Even#PhMusc	#A3CC7A
Stomatointestinal muscle	2	Stomatoint_Muscle	#005200
Vulval muscle cells	8	Vulval_Muscle	#7AA352
Uterine muscle cells	8	Uterine_Muscle	#7AA300
Sphincter & anal depressor muscle	3	Sphnc_&_Anal_Dep_Musc	#527A00
Sensory neurons	~60	SensoryNeuron	#CC52BE
Interneurons	~80	Interneuron	#CC2900
Motor neurons	~120	Motor_Neuron	#7A52BE
Polymodal neurons	~10	PolymodalNeuron	#C40202
Neurons (unknown function)	~32	NeurUnkFunc	#7A0029
Hypodermal cells (hyp1-hyp11, P cells)	~30	Hypodermis	#B09C8A
Seam cells (H, V, T lineages)	16	Seam_Cell	#A35229
Intestinal cells (int1-int9)	20	Intestine	#CCA3CC
Pharyngeal epithelial cells	~10	Pharyngeal_Epithelium	#7A5252
Rectal epithelial cells	~6	Rectal_epithelium	#7A5252
Vulval epithelial cells	~22	Vulva_epithelium	#7A7ACC
Arcade cells	~6	Arcade_Cells	#A3A300
Socket cells	~20	SocketCell	#CC7A7A
Sheath cells	~10	SheathOther	#297A7A
GLR cells	6	GLR_Cells	#BE7A00
Marginal cells (mc1-mc3)	~9	marginal_cells	#BE29BE
Head mesodermal cell	1	Head_Mesodermal_Cell	#CC5229
Coelomocytes	6	Coelomocyte	#CCA300
Excretory cell	1	Excretory_Cell	#A32952
Excretory pore cell	1	Excretory_Pore_Cell	#BDC672
Excretory duct cell	1	Excretory_Duct_Cell	#A37A52
Excretory gland cells	2	Excretory_Gland_Cells	#7A7AA3
Germline (syncytial)	~1000*	Germline	#002952
DTC & somatic gonad	~12	DTC_&_Somatic_Gonad	#7A52CC
Spermatheca	~24	Spermatheca	#297ACC
Spermathecal-uterine valve	~4	Spermath_Uterin_Valve	#52527A
Uterus (non-muscle)	~12	Uterus	#7AA3A3
Pharyngeal & rectal glands	~9	Phary_&_Rect_Glands	#A3A3CC
VPI & VIR cells	~6	VPI_&_VIR	#7A5229

*Germline contains ~1000 germ cells but is treated as a syncytial tissue for visualization purposes.

Cells not in the above table: Any cell not explicitly listed is assigned to the closest tissue-type material based on its WBbt lineage. The DD004/DD008 integration pipeline resolves this mapping. If a cell has no WBbt annotation, it defaults to Hypodermis (#B09C8A) — the most common non-specific tissue.

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8. Alternatives Considered

1. Flat / Cartoon Rendering Style (Cell Shading)

Rejected. Cel-shaded or flat-color rendering produces clean, illustrative visuals but does not convey biological depth. Translucency, subsurface scattering, and volumetric effects are essential for communicating that this is a living organism, not a diagram. Flat rendering also eliminates the lighting cues needed for 3D perception.

2. Photorealistic Rendering (Path Tracing)

Rejected. Path-traced rendering produces beautiful results but is computationally prohibitive for real-time playback at 60fps, even with WebGPU. It also risks the uncanny valley — a "almost real" worm that looks slightly wrong is worse than a clearly stylized rendering that communicates the right information. PBR with bloom and OIT achieves a "scientifically evocative" look without the performance cost.

3. False-Color Only (No Surface Rendering)

Rejected. Displaying only colormapped data (like a heatmap overlaid on wireframe) communicates quantitative information but not anatomy. A non-scientist cannot identify structures or understand spatial relationships. The smooth-surface organism scale is essential for the "a person can see it's a worm" criterion.

4. Per-Cell Unique Colors (959 Distinct Hues)

Rejected. Assigning a unique color to each of the 959 cells would make the tissue-type grouping invisible. The human visual system cannot distinguish 959 colors. The 37-material-category approach groups cells by tissue type, which is biologically meaningful and visually parseable.

5. Dynamic Color Palette Based on Data Range

Considered for future. An auto-scaling palette that adjusts color ranges based on actual simulation data min/max could improve contrast. However, it makes visual comparison across simulations inconsistent. The fixed scales in Section 1B (e.g., -80mV to +20mV for voltage) match physiological ranges and produce consistent visuals regardless of simulation output.

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9. Quality Criteria

1. Every cell type has a color. All 37 Virtual Worm material categories are implemented. Any cell visible in the viewer is colored according to its tissue-type mapping (Section 7).

2. Worm recognition. A non-scientist shown the organism-scale view (Mockup 1) can identify "that's a worm" without prompting.

3. Activity discrimination. Active vs. resting neurons are visually distinguishable at 1080p resolution. An observer can point to the "glowing" neuron in a field of 302.

4. Muscle state visible. Contracted (red) vs. relaxed (green) muscles are distinguishable in the tissue-scale view (Mockup 3). The locomotion wave pattern is visible as alternating color bands.

5. Molecular communication — membrane. The molecular-scale membrane view (Mockup 10) communicates "this is a cell membrane with channels" to a biology undergraduate. Ion channels, lipid bilayer, and flowing ions are identifiable.

6. Molecular communication — gene expression. The molecular-scale intracellular view (Mockups 13-14) communicates the central dogma: a user can watch a gene being transcribed in the nucleus, see the mRNA travel to the ER, watch a ribosome build a channel protein, and see the finished channel arrive at the membrane. The full pipeline is visually traceable in a single session.

7. Scale transitions are smooth. The organism→tissue transition (Mockup 12) does not produce visual artifacts, sudden pops, or disorienting jumps. A user can smoothly zoom from organism to molecular scale.

8. CeNGEN-driven expression. The gene expression pipeline at molecular scale reflects the selected cell's actual expression profile from DD005 CeNGEN data — a motor neuron produces different channel types than a sensory neuron.

9. Reference mockup match. All 14 mockups have corresponding implementation screenshots that match the specifications. Deviations are documented and justified.

10. Performance. Rendering meets the targets in Section 5F (60fps target, 15fps minimum on integrated GPU) at all three scales.

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10. Boundaries

This document does NOT specify:

• Data formats or schemas — See DD014 (OME-Zarr structure, .zattrs metadata)
• Viewer UI layout or interaction design — See DD014 (layout mockup, layer toggle system, inspector panel)
• Docker deployment or CI/CD — See DD014 + DD013
• Simulation algorithms — See DD001-DD009
• Validation criteria — See DD010
• Web framework choice (Trame vs Three.js) — See DD014

DD014.1 specifies purely: what things look like, what color they are, how they glow, how they transition between scales, and what the rendering algorithms are.

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Context & Background

Scientific visualization requires consistent, meaningful color coding to communicate biological data accurately. Medical and scientific illustration conventions (e.g., Netter atlas color traditions, electrophysiology colormaps) inform palette choices throughout this specification.

The Virtual Worm project (2012) established the only canonical color palette for C. elegans anatomy, defining 37 material categories in a Blender model. This specification preserves those heritage colors as the foundation and extends them with activity-state overlays and molecular-scale assignments. Ensuring visual consistency across all OpenWorm renderings, publications, and documentation screenshots is essential for project identity and scientific communication.

The rendering techniques specified here (PBR materials, bloom, OIT, volumetric ray marching) represent a balance between visual quality and real-time performance. They were selected to run at 60fps on commodity hardware while communicating biological structure at three distinct spatial scales.

References

1. Virtual Worm Blender Model (February 2012): Virtual_Worm_February_2012.blend — Source of 37 canonical material categories. MTL file: Virtual_Worm_February_2012.mtl.
2. DD014: Dynamic Visualization Architecture: Companion document specifying data pipeline, Zarr schema, viewer framework, and Docker integration.
3. McGuire & Bavoil (2013): "Weighted Blended Order-Independent Transparency" — Algorithm for OIT compositing (Section 5A).
4. Three.js MeshStandardMaterial: https://threejs.org/docs/#api/en/materials/MeshStandardMaterial — PBR material model reference.
5. CeNGEN (2020-2024): C. elegans Neuronal Gene Expression Map — Source for cell-type-specific channel densities referenced in molecular scale.
6. WormBase cell ontology (WBbt): https://wormbase.org — Canonical cell identity assignments used for cell-to-material mapping.
7. WormAtlas: https://wormatlas.org — Anatomical reference for tissue structure and cell positions.

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Integration Contract

Inputs / Outputs

Direction	Source/Consumer	Data	Format
Input	DD014	Simulation state data	OME-Zarr
Output	Viewer	Rendered frames	WebGL/PNG

Configuration

• Color palette: defined as JSON/YAML theme file consumed by DD014 viewer
• Rendering parameters: ambient occlusion radius, SSS depth, bloom threshold

Coupling Dependencies

• Upstream: DD014 (viewer architecture), DD005 (cell type list determines color assignments)
• Downstream: All visualization outputs, publications, documentation screenshots

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• Approved by: Pending
• Implementation Status: Proposed

• Next Actions:

• Validate hex values against Virtual Worm Blender model (re-export MTL and cross-check)

• Create reference mockup images (Blender renders or concept art) for the 14 canonical views
• Implement heritage palette in Worm3DViewer (Phase 1) — replace current ad-hoc colors with Section 1A
• Implement voltage-to-visual mapping (Section 1B) in the neuron rendering pipeline
• Review with community: do the molecular-scale visual choices (Section 3C) communicate biology effectively?
• Map DD005 CeNGEN expression data to per-cell-type gene expression visualization parameters (which genes are visually transcribed, at what rate)
• Design data pipeline for gene expression events (transcription → export → translation → trafficking) — may require new Zarr group in DD014 schema