# fruitFly A whole fruit fly nervous system running as a spiking network on the GPU, a fly body it drives, and a bench for experiments on it. Install this package and a world holds the complete adult male *Drosophila* central nervous system (MaleCNS v1.0: 164,587 neurons, 25.6 million connections, CC-BY 4.0) as a leaky integrate-and-fire network you can stimulate, silence, read out and watch, plus a fly whose taste, looming, walking, turning, feeding, flight and escape run through that wiring. ## Contents The network: - `maleCNS.connectome/` is MaleCNS v1.0 packed for the GPU (109 MB, the edge table in two parts). It is an instance of the `connectome` asset type, which lives at the world root (`/zero/source/connectome.assetType/`) and travels with the package as a dependency: any nervous system's wiring as one asset (`manifest.json`, `neurons.bin`, `offsets.bin`, `edges.bin` or its parts). `guides { path = "types/connectome" }` is the reference. - `lif_integrate`, `lif_propagate`, `lif_clear`, `lif_reset` (`.computeShader`) are the four kernels of the network: membrane step, event-driven spike propagation over the CSR edge table, step close, reset. - `brain.module/` is `Brain.load(connectomeRef, params)`, which binds a connectome to the kernels and returns the network: `step`, `update`, `select`, `stimulate`, `silence`, `watch`, `rates`, `activity`, `classRates`, `groupActivity`, `drives` and the cloud. - `FruitFlyBrain.component/` puts a network on an entity: it loads the connectome the `connectome` field names, steps it every frame, draws the cloud, and exposes `stimulate` / `silence` / `watch` / `rates` / `reset` (the first three are synced, so every peer's copy receives the same inputs). - `neuron.shader/`, `neuron.material/` and `cloud_gather.computeShader/` are the instanced neuron cloud, each neuron lit by its own activity. - `crackle.soundClip/` is the network's own sound: a sparse crackle that is silent when the network is silent and a hiss when it runs away. The fly: - `flyBody.module/` is the fly's body as an entity tree with a tripod gait, wings, proboscis and a hop. - `FruitFly.component/` is the embodied fly: it reads the world into the brain's sensory neurons and reads motor commands back out of named cell types. - `FoodPatch.component/` is a disc of food on the ground the fly can taste. - `wing.material/`, `eye.material/` and the `wingbeat`, `feed` and `jump` sound clips are what the fly looks and sounds like. The instrument: - `FruitFlyLab.component/` is the bench window: network state and knobs, live readouts with traces and rasters, hot classes, live drives, a neuron panel, a legend, and a selection line to stimulate, silence, restore, count or watch any set of neurons. - `selection.module/` is the selection grammar the bench and everything else parse with. - `protocol.module/` is the guide's experiments as records anything can run, and the verdict a run computes from its own numbers. - `FruitFlyExperiments.component/` is the experiments panel: those protocols with one press each, a run list, a compare overlay and a verdict line. - `FirstRun.component/` is the four-step card that walks a newcomer from a reset network to a proboscis coming out. - `lab.inputMap/` and `experiments.inputMap/` are the bench's and the panel's controls, each binding keyboard, gamepad and touch. - `experiments.guide/` is the bench manual and the five experiments. The lab around it: - `labFloor.material/` and `FruitFlyLook.component/` are the floor, the fog, the vignette and the lighting intent, held as data rather than as code. - `arenaRing.mesh/` is the ring on the floor the fly stays inside. ## Usage ```luau -- The brain: one entity, one network. The default connectome is maleCNS. local brainEnt = entity.spawn("Brain") brainEnt.position = { 0, 6, -8 } brainEnt.component.add("FruitFlyBrain", { gain = 0.6, timeScale = 1 }) -- An embodied fly driven by it, and something for it to taste. local fly = entity.spawn("Fly") fly.component.add("FruitFly", { brain = brainEnt, bodyLength = 0.6 }) local food = entity.spawn("Food") food.position = { 3, 0, 0 } food.component.add("FoodPatch", { radius = 0.6, sugar = 1 }) -- The bench, the experiments panel and the card. entity.spawn("Lab").component.add("FruitFlyLab", { brain = brainEnt, fly = fly }) entity.spawn("Experiments").component.add("FruitFlyExperiments", { brain = brainEnt, fly = fly }) entity.spawn("FirstRun").component.add("FirstRun", { brain = brainEnt, fly = fly }) -- Or from code: local comp = brainEnt.component.get("FruitFlyBrain") comp:watch("MN9", { types = { "MN9" } }) -- proboscis motor neurons comp:stimulate({ types = { "claw_tpGRN" } }, 100) -- tarsal taste pegs at 100 Hz print(comp:rates().MN9) -- Hz per neuron, updated every frame ``` A selection names neurons by the dataset's own vocabulary: `types` (exact cell-type names), `typePrefix`, `pattern` (a Lua pattern over the type name), `classes`, `superclasses`, `sides` (`L`/`R`/`M`), `excitatory`, `indices`, `limit`. `brain:info(i)` answers what any neuron is. ## The model Every neuron is a leaky integrate-and-fire unit with the constants Shiu et al. 2024 (Nature) fitted to the FlyWire brain: rest and reset at -52 mV, threshold -45 mV, membrane time constant 20 ms, synaptic time constant 5 ms, refractory period 2.2 ms, transmission delay 1.8 ms, 0.275 mV per synapse. A presynaptic neuron whose consensus transmitter is GABA, glutamate or histamine inhibits; every other transmitter excites. A connection carries its synapse count; connections under `minSynapses` (default 5) carry nothing. `gain` scales every synapse. MaleCNS traces about 2.5 times the synapses per connection FlyWire does, so at gain 1 the network runs away under any drive; at 0.6 (the default) driving the 50 tarsal taste-peg neurons at 100 Hz holds the proboscis motor neurons MN9 at about 115 Hz while the Kenyon cells stay under 0.1 Hz, and driving the 595 Johnston's organ neurons instead leaves MN9 at zero. At 0.5 the taste drive reaches nothing. The bench's gain slider is the experiment, and the experiments panel's "Gain recovery" runs all three in one press. Everything runs on the GPU: the state, the input ring, the spike list and the edge table. The CPU sees the per-group spike counters each frame and, on request, the per-neuron activity lane. Integer atomics make a step order-independent, so two peers stepping the same inputs read the same network. ## The fly `FruitFly` reads named cell types out of the brain and writes the world into others; every name is in `FruitFly.component/init.luau`: | command | cell types | |---|---| | walk | the leg motor neurons (`vnc_motor` types ending in ` MN`), per side | | turn | `DNa01`, `DNa02` left minus right | | proboscis | `MN9` | | flight | the wing power-muscle motor neurons (`DLMn`, `DVMn`) | | jump | a `DNp01` (giant fibre) burst | | sense | cell types | driven by | |---|---|---| | tarsal taste | `claw_tpGRN`, `dorsal_tpGRN`, per side | that side's front foot on a `FoodPatch` | | labellar taste | `LB*` labellar bristle GRNs | the extended proboscis on a `FoodPatch` | | looming, LPLC2 path | `LPLC2` | a player's avatar growing fast in front of the fly | | looming, LC4 path | `LC4` | the same, driven as a separate path so one can be silenced | The two looming paths are driven separately and weighted by how head-on the approach is, so an avatar walking up behind the fly does not loom and silencing one detector class is an experiment with an answer. The body moves kinematically at `walkSpeed` body lengths per second; the fly faces its entity's -Z. On a shared world the entity's owner writes the senses into the brain (a synced call) and every peer poses its own copy from its own network. ## Controls | Action | Keyboard | Gamepad | Touch | |---|---|---|---| | Bench: show or hide | L | Start | The "Lab" button | | Bench: move focus | Down and Up, Tab | D-pad down and up | Tap the control | | Bench: activate the focused control | Enter | North (Y) | Tap | | Bench: nudge the focused slider | Left and Right | D-pad left and right | Drag it | | Bench: identify a neuron | Click it in the cloud | West (X) | Tap it | | Experiments: show or hide | P | Select | The "Experiments" button | | Experiments: next protocol | N | Right stick press | Tap the protocol | | Experiments: previous protocol | B | None: the list wraps | Tap the protocol | | Experiments: run | R | Right trigger | RUN | | Experiments: compare | C | Left trigger | COMPARE | Both maps name their controls apart (`lab*` and `exp*`) and take disjoint keys and buttons, so the bench and the panel can be open together and neither answers for the other. ## Data and license MaleCNS v1.0: HHMI Janelia FlyEM, Google Research and the Cambridge connectomics group, released 8 June 2026 (Berg et al. 2026, Cell, doi:10.1016/j.cell.2026.08.015), CC-BY 4.0. The pack was written by a script that reads the public flat-connectome export (`connectome-weights ... traced-only`, body annotations, consensus neurotransmitters), assigns dense indices, sorts edges by presynaptic neuron and writes the four files `types/connectome` describes; the manifest carries each source file's SHA-256. ## Notes - Loading the network reads the 102 MB edge table into a GPU buffer once per `FruitFlyBrain`; the VFS copy is released afterwards. - The neuron cloud is one instanced draw of every neuron with a soma (139,741). Its transforms are static; the activity lanes are written by the integrate kernel. - `maxStepsPerFrame` bounds GPU time per frame; at 32 steps of 1 ms a 60 fps engine keeps up with real time. - A neuron reads out under at most three groups at once. The fly holds seven of its own and the protocols watch five more under the guide's names, so a bench watch of the same cell types under the same name shares the group rather than spending another slot.

# FruitFlyBrain A whole connectome running as a spiking network on this entity. It loads the `connectome` asset the field names (the package's `maleCNS` by default), steps it every frame the gameplay clock runs and, with `runInEdit`, in edit mode too; draws every neuron with a soma as a lit point around the entity; plays the network's own crackle from it; and hands the live network to anything that asks. Fields: `connectome`, `running`, `runInEdit`, `timeScale`, `maxStepsPerFrame`, `gain`, `minSynapses`, `showCloud`, `cloudGate`, `cloudScale`, `neuronRadius`, `bloom`, `bloomIntensity`, `crackle`. The defaults are the calibrated regime: gain 0.6, minSynapses 5, timeScale 1, maxStepsPerFrame 32. Methods on the ref: `getBrain()`, `stimulate(sel, hz, source?)`, `silence(sel, on)`, `clearStimulation(source?)`, `drives()`, `reset()`, `watch(name, sel)`, `unwatch(name)`, `rates()`, `classRates(limit?)`, `groupActivity(name)`, `neuronAt(screenX, screenY, radiusPx?)`, `keepCloudDrawn(seconds?)`, `describe()`. `stimulate`, `silence`, `clearStimulation` and `reset` are synced calls, so every peer's copy of the network receives the same inputs. `onLoaded` fires with the neuron and edge counts once the network is on the GPU. ```luau local e = entity.spawn("Brain") e.position = { 0, 5, -8 } e.component.add("FruitFlyBrain", { gain = 0.6 }) local c = e.component.get("FruitFlyBrain") c:watch("MN9", { types = { "MN9" } }) c:stimulate({ types = { "claw_tpGRN" } }, 100, "bench") ``` ## The visibility gate, and what it means for a capture The cloud is 139,741 instances, and a registered instanced population has its whole transform run recomposed on the CPU every frame whether or not the cull draws any of it. Measured on this world: `render.mesh_transform_compose` is 4.74 ms a frame with the cloud registered and 0.67 ms with it down. So the component tests the cloud's bounding sphere against the on-screen camera's frustum every three frames, registers the draw the moment the sphere enters, and drops it after thirty consecutive frames outside. `showCloud = false` still takes everything down. The gate only knows about the camera on screen. **An offscreen capture aimed at the brain from a station the player is not standing at can therefore come back with no cloud in it.** Call `keepCloudDrawn(seconds)` first, or set `cloudGate` false. Moving the entity moves the cloud with it: the transforms are rewritten from the neuron records a slice a frame, with no rebuild. ## Drives are owned `stimulate` takes the name of whoever is driving. The rate a neuron sees is the largest any source asked for, so the fly stepping onto a food patch (`"fly"`) cannot take away what the bench (`"bench"`) or a protocol (`"protocol"`) is driving, and `clearStimulation("fly")` clears only the fly's. A call that names no source is recorded as `"code"`. `drives()` is what the bench lists. ## Sound and light While the cloud is drawn the component registers the builtin bloom on the `scene` layer, which is what turns a spiking neuron from a bright dot into a point of light, and takes it off again when the cloud goes down. The Audio component it puts on the entity plays the package's `crackle` clip on a loop with its volume following the whole-network rate: silent below 0.05 Hz, rising to 0.35 by 5 Hz.

# protocol The experiments from `experiments.guide` as records anything can run, and the verdict a run computes from its own numbers. `Protocol.all()` is the five. `Protocol.variants(proto)` turns one into its runnable forms, one per variant. `Protocol.run(brainComp, proto, onDone)` starts a run and `Protocol.tick(run)` advances it, once a frame, until it reports itself done. Nothing in here spawns a task, so a run cannot outlive whoever is ticking it. ```luau local Protocol = require("~.protocol") local comp = entity.find("Brain").component.get("FruitFlyBrain") local form = Protocol.variants(Protocol.byId("taste"))[1] local run = Protocol.run(comp, form) -- from update(dt), every frame: if Protocol.tick(run) then print(run.verdict) -- MN9 peaked 130 Hz at 2497 ms, held 112 Hz; Kenyon_Cell 0.023 Hz; -- network mean 1.30 Hz, 1.30 over baseline (confined) end ``` A run starts from rest: it clears every drive and resets every membrane, so the state the network was left in cannot reach its numbers. It then records `Protocol.BASELINE_MS` of the network before its first drive: the fly is alive while a protocol runs and what it drives through its own sensory neurons is part of the network's rate, and the readouts need about a second of the network's own clock before they report the reset network rather than the one before it. The verdict's spread word is computed on the rate the drive ADDED to that baseline, so an experiment reads the same whether the fly is standing still or seeing the arena wall loom. A protocol's `durationMs` is the length of its drive phase; the lead-in is on top of it, and a peak's time is reported from the moment the drive started. It applies its own gain and minimum synapse count for the length of the run and puts the previous values back. It silences what it ablates and restores it. It stops its own drives by driving them at 0 Hz, so no other drive is touched. Readouts are watched under the names the guide uses (MN9, Kenyon_Cell, DNp01, LPLC2, LC4), so a bench watching the same cell types under the same name shares the group rather than spending a second readout slot on each neuron. `FruitFlyExperiments` is the panel that runs these, and `FirstRun` is the card that walks a newcomer to the first result. Both require this module, and the `Protocol.ui` table is how they talk to each other.