# Protocols


The curriculum is organized into six modules that progressively build
from developmental neurobiology and optogenetics to connectomics and
complex behavior. Each module includes detailed protocols, guiding
questions, and references to primary literature.

### [Developmental Logic as Circuit Blueprint](hemilineage.qmd)

How do developmental building blocks give rise to functional neural
circuits? In this module, students optogenetically activate
hemilineage-defined neuronal populations in the *Drosophila* larval
ventral nerve cord and test whether developmental origin predicts
behavioral output. A companion connectomics session links the observed
behaviors to circuit architecture using Neuroglancer.

### [Exploring Descending Neurons within the Brain](catmaid01.qmd)

What can the morphology and connectivity of individual neurons tell us
about their function? Students use CATMAID to navigate the first-instar
larval connectome, visualize descending neurons, map their synaptic
partners, and generate hypotheses about how brain commands reach the
motor system.

### [Exploring Lineages in the Larval VNC](catmaid02.qmd)

How does birth order within a neuronal lineage shape circuit membership?
Students pick a neuroblast lineage, trace its progeny in CATMAID, and
investigate whether early-born and late-born neurons differ in their
morphology, connectivity, and potential roles in sensory versus motor
processing.

### [Intro to Optogenetics](optogenetics.qmd)

How can we test whether a specific set of neurons is sufficient to drive
a behavior? This hands-on module introduces the GAL4/UAS system and
channelrhodopsin-based optogenetics. Students activate targeted neurons
in *Drosophila* larvae with light, quantify evoked behaviors, and
compare experimental and control animals.

### [Sensory Processing to Sequential Action Control](hierarchy_student.qmd)

How do sensory signals get transformed into organized sequences of
actions? Students set up genetic crosses, prepare flies for optogenetic
or thermogenetic activation, and explore how different driver lines
recruit distinct nodes in the sensorimotor hierarchy — from sensory
interneurons to descending command-like neurons.

### [Aggression in *Drosophila melanogaster*](aggression.qmd)

How can complex social behaviors be quantified and dissected? Students
build fighting chambers, record aggression assays between male flies,
and learn to design automated behavioral classifiers using tools like
JAABA and FlyTracker and bridge circuit manipulation with rigorous
behavioral analysis.

### [Sleep in *Drosophila melanogaster*](sleep.qmd)

How can internal states like sleep be measured and manipulated? Students
monitor activity and rest patterns, analyze sleep metrics such as bout
length and latency, and explore how neural circuits and environmental
cues regulate sleep. Students learn to link behavior to underlying
physiological and circuit mechanisms.