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Chiang, A.-S.

Publications and source records attributed to Chiang, A.-S..

18 recordsLinked to original sources

Long-term memory performance optimization via Neural network-based curve fitting in Drosophila

Long-term memory (LTM) formation typically requires extensive training or highly salient experiences, limiting learning efficiency. Operant conditioning is generally thought to produce stronger memory than classical conditioning because of its active learning component. Unexpectedly, however, laser-based social conditioning in Drosophila melanogaster revealed that while classical paradigms yielded lower short-term memory (STM) scores but higher LTM retention, operant paradigms exhibited higher STM scores followed by rapid LTM decay. To resolve this discrepancy, we employed the AI Complex Systems Response (AI-CSR) framework, which reconstructs high-dimensional learning landscapes from sparse sampling and predicts globally optimal training conditions. Following AI-CSR optimization, operant conditioning produced a twofold increase in LTM scores, yielding the strongest 24-hour social memory performance reported in flies to date and revealing the expected superiority of active learning, which had conversely shown poorer performance under standard training protocols. In contrast, AI-CSR did not further enhance classical conditioning performance but reduced training time by 50%. Single-cell RNA sequencing revealed expanded neuronal recruitment marked by the activation and inhibition of various gene combinations. Together, these findings link circuit-level reorganization with molecular programs underlying efficient long-term memory and demonstrate how AI-guided optimization can uncover latent learning capacity in biological systems.

animal behavior and cognition↗

High-resolution volumetric intravital imaging reveals asymmetric serotonin-dependent post-shock activity in the Drosophila brain

Volumetric intravital imaging of adult Drosophila brains remains challenging due to optical scattering and speed limitations of conventional microscopy. Here, we present V-shape Bessel-beam light-sheet microscopy (vSPIM), an upright, high-speed platform achieving subcellular resolution across large, opaque volumes in vivo. Through real-time calcium imaging in adult Drosophila, vSPIM uncovered two unprecedented phenomena: first, a complex ensemble of approximately 150 olfactory projection neuron boutons (more than 400 per hemisphere) resolved 18 distinct odor valence coding patterns within the dense mushroom body calyx, aligning with connectomic architecture. Second, vSPIM revealed a previously uncharacterized asymmetric, serotonin-dependent post-shock firing (PsF) response. This PsF activity emerged within the mushroom body and dopaminergic neurons only after repetitive aversive stimulation, distinct from canonical dopamine-driven reinforcement signals. Finally, we demonstrated the versatility of vSPIM by tracking corneal endothelial dynamics during mouse wound healing. Overall, vSPIM establishes a scalable framework for intravital imaging, bridging the gap between optical innovation and circuit physiology in adult tissues.

neuroscience↗

Robust volumetric multiplex staining of centimeter-scale FFPE tissues guided by neural network-based optimization

Archived formalin-fixed, paraffin-embedded (FFPE) tissues, including brain-bank specimens, are valuable resources for disease research, but rapid cyclic immunolabeling of intact specimens remains challenging. Here, we present FIDELITY, an epoxy-free workflow that balances optical transparency, immunostaining performance, and tissue integrity for multi-cycle protein profiling in centimeter-thick FFPE specimens. Neural network-guided optimization identified an SDS-glycine formulation that integrates delipidation and epitope retrieval while preserving tissue stiffness, replacing prolonged epoxy reinforcement and subsequent high-temperature antigen retrieval with a single aqueous pretreatment. Application to human Alzheimer's disease specimens enabled volumetric imaging and quantitative analysis while retaining compatibility with conventional histopathology. Its compatibility with active electrophoretic staining further supported rapid labeling and five rounds of immunolabeling in a whole FFPE mouse brain. Two-round labeling of a human glioma specimen further demonstrated the applicability of the cyclic workflow to human pathological tissue. Together, FIDELITY provides a practical platform for large-volume, multiplexed protein profiling of intact FFPE specimens.

neuroscience↗

Latent-centric Isotropic Resolution Enhancement for Expansion Microscopy Imaging via Neural Compression and Self-supervised Learning

Expansion microscopy (ExM) enables nanoscale imaging for disease characterization. However, whole-organ analyses remain limited by several challenges. Current super-resolution methods either require high-resolution ground-truth data or assume spatially uniform point spread functions--assumptions that rarely hold in whole-organ imaging with depth-varying aberrations and illumination drift. Existing methods also worsen storage demands by inflating already multi-terabyte datasets without using neural compression. We propose a single-stage, self-supervised framework that addresses both resolution anisotropy and storage constraints through compression-aware isotropic super-resolution. Our approach combines a 2D lateral encoder that operates directly on raw slices to avoid memory limits with a lightweight volumetric decoder that preserves cross-slice continuity. A vector-quantized variational autoencoder (VQ-VAE) provides an information-sufficient bottleneck, achieving up to 128x slice compression and up to 8x axial resolution enhancement. This latent-centric design yields approximately 1000x reduction in storage compared with storing fully isotropic volumes. The framework achieves higher GPU throughput, lower memory usage, and stronger multi-GPU scalability than prior methods. By designating compressed latent space as the native storage format, it enables efficient on-demand isotropic reconstruction directly from compact representations. This combination of isotropic enhancement and neural compression framework therefore makes large-scale, whole-organ ExM analysis practical while maintaining analysis-ready accessibility, addressing a bottleneck in translating ExM to clinical biomarker discovery.

bioinformatics↗

Dopaminergic Modulation of Mushroom Body Output Neurons Mediates Nociception-Induced Escape in Drosophila

In Drosophila, noxious heat is detected by peripheral nociceptors expressing transient receptor potential (TRP) channels, including Painless and TrpA1, and rapidly triggers escape behavior. Although peripheral transduction has been defined in detail, the central circuits and neuromodulatory mechanisms that translate nociceptor activity into escape decisions remain poorly understood. Here, we combine targeted behavioral perturbations with anatomical tracing to delineate a nociception-to-escape pathway that engages dopaminergic modulation of mushroom body (MB) output. Kir2.1-mediated silencing across candidate neurotransmitter systems revealed a specific requirement for MB-innervating dopaminergic neurons (DANs)--particularly subsets within the protocerebral posterior lateral 1 (PPL1) and protocerebral anterior medial (PAM) clusters--for robust nociception-induced escape. Anterograde trans-Tango tracing from painless- and trpA1-expressing nociceptors labeled these MB dopaminergic neurons as direct postsynaptic partners, consistent with convergence of distinct nociceptor inputs onto a shared dopaminergic pathway. Finally, silencing a subset of mushroom body output neurons (MBONs) delayed escape without overtly disrupting baseline locomotion, supporting a model in which dopaminergic signaling recruits MB output to shape defensive action selection. Together, our results define a multi-layer circuit motif linking peripheral nociception to MB-dependent escape and provide a framework for dissecting how neuromodulation gates rapid defensive behaviors.

neuroscience↗

Pak, a downstream gene of ecdysone signaling, determines left-right polarity in the Drosophila brain through neuronal cell chirality

Left-right (LR) asymmetry is a conserved characteristic of the brain in various animals and is related to its higher-order functions. The Drosophila brain has an LR asymmetric structure known as an asymmetrical body (AB). LR asymmetric neurite remodeling lateralizes the AB, and ecdysone signaling determines LR specificity. However, the mechanisms underlying LR specificity remain unclear. We found that the Slit/Dreadlocks/Roundabout/p21-activated kinase (Pak) signaling axis determines the LR polarity of the AB downstream of ecdysone signaling in the type II neuroblast lineage before LR asymmetric neurite remodeling. In Drosophila, the intrinsic chirality of cells (cell chirality) defines the LR asymmetry of various non-neuronal organs. We suggested that neurons derived from type II neuroblasts exhibit cell chirality, which is established through Pak and ecdysone signaling and determines the LR polarity of the AB. As cell chirality is broadly observed in eukaryotes, our study reveals a novel mechanism underlying LR asymmetry of the brain.

neuroscience↗

Unique Asymmetric Branching of Drosophila Neurons Optimizes Temporal Dendritic Computation

Neurons execute a versatile array of computations through a complex interplay of factors, including their morphology and synaptic architecture. Dendritic branching encodes upstream inputs into diverse spike patterns transmitted via downstream axons. While earlier studies highlighted the distinct morphologies and functions of a few representative neurons, the availability of large-scale electron microscopy and fluorescent imaging now enables comprehensive data analysis and further simulations to explore structure-function relationships more broadly. This study investigates the general morphological characteristics of diverse neuron types in the fly model. By employing the Strahler Order (SO) metric, we identified a specific bias towards asymmetry in neuronal branching and further investigated the effect of the asymmetry on computational capabilities. Specifically, symmetric branching enhances coincidence detection capability, whereas asymmetric branching increases input order-selectivity. While certain neurons exhibit extreme symmetry or asymmetry optimized for specific tasks, most neurons strike a balance between these computational strategies. This balance underscores the intricate relationship between neuronal structure and function. In contrast to the wide range of branching symmetries found in random bifurcation models, neurons across different species exhibit species-specific asymmetry, suggesting shared underlying branching mechanisms. Our findings provide a fresh perspective on the exploration of neuronal morphologies and their computational roles. Significance StatementThis study reveals a novel structure-function relationship by analyzing the asymmetric branching patterns of fly neurons using extensive morphological data. While certain neurons display extreme symmetry or asymmetry for specialized computational roles, most converge toward a characteristic degree of asymmetry to balance their computational demands, especially in larger branching structures. This suggests that neuronal branching may be governed by intrinsic principles that support both developmental and functional needs.

neuroscience↗

Hybrid Neural Networks of the Olfactory Learning Center in the Drosophila Brain

Biological signal encoding is shaped by the underlying neural circuitry. In Drosophila melanogaster, the mushroom body (MB) houses thousands of Kenyon cells (KCs) that process olfactory signals from hundreds of projection neurons (PNs). Previous studies debated the connectivity between PNs and KCs (random vs. structured). Our multiscale analysis of electron microscopic data revealed a hybrid network with diverse synaptic connection preferences and input divergence across different KC classes. Using MB connectome data, our simulation model, validated via functional imaging, accurately predicted distinct chemical sensitivities in the major KC classes. The model suggests that the hybrid network excels in detecting food odors while maintaining precise odor discrimination in different KC classes. These findings underscore the computational advantages of this hybrid network.

neuroscience↗

BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology

BigNeuron is an open community bench-testing platform combining the expertise of neuroscientists and computer scientists toward the goal of setting open standards for accurate and fast automatic neuron reconstruction. The project gathered a diverse set of image volumes across several species representative of the data obtained in most neuroscience laboratories interested in neuron reconstruction. Here we report generated gold standard manual annotations for a selected subset of the available imaging datasets and quantified reconstruction quality for 35 automatic reconstruction algorithms. Together with image quality features, the data were pooled in an interactive web application that allows users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and reconstruction data, and benchmarking of automatic reconstruction algorithms in user-defined data subsets. Our results show that image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. By benchmarking automatic reconstruction algorithms, we observed that diverse algorithms can provide complementary information toward obtaining accurate results and developed a novel algorithm to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms. Finally, to aid users in predicting the most accurate automatic reconstruction results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic reconstructions.

bioinformatics↗

CREB repressor in mushroom body enhances Drosophila LTM formation

Long-term memory (LTM) requires learning-induced synthesis of new proteins allocated to specific neurons and synapses in a neural circuit. Not all learned information, however, becomes permanent memory. How the brain gates relevant information into LTM remains unclear. In Drosophila adults, a single training session in an olfactory aversive task is not sufficient to induce protein synthesis-dependent LTM. Instead, multiple spaced training sessions are required. Here, we report that initial learning induces neural activity in the early /{beta} subset of Kenyon cells of the mushroom body (MB), and output from these neurons inhibits LTM formation. Specifically in response to spaced training, Schnurri activates CREBB expression which then appears to suppress the inhibitory output from MB. One training session can enhance LTM formation when this inhibitory effect is relieved. We propose that learning-induced protein synthesis and spaced training-induced CREBB act antagonistically to modulate output from early /{beta} MB neurons during LTM formation.

neuroscience↗

CyDAP-A fluorescent probe for cytosolic dopamine detection

Dopamine (DA) is an essential neurotransmitter modulating motor and cognitive functions. Several neurological disorders, including Parkinsons disease (PD) and drug addiction, are the result of DA system dysfunction; however, it remains incomplete understood of why DA neuron is selectively more vulnerable than other neurons. Here we utilize the spectral feature of human MAO B (monoamine oxidase B) to design a genetic-amenable, GFP-based fluorescent probe CyDAP. Upon genetic and pharmacological manipulations to elevate the cytosolic DA levels in cells and Drosophila models, CyDAP shows enhanced GFP emission, suggesting this probe is feasible for DA detection. Furthermore, we observe that expressing human -Synuclein in Drosophila elicited GFP emission from CyDAP, suggesting a link between cytosolic DA imbalance and regional vulnerability in PD context. Importantly, CyDAP can detect the change of cytosolic DA in live Drosophila brains, as demonstrated by time-lapse and the 4D light-sheet confocal recording. CyDAP may serve as a tool for evaluating metabolic deregulation of DA in brain models of PD and other DA system-related psychiatric disorders.

neuroscience↗

The Fruit Fly Brain Observatory: From Structure to Function

The fruit fly is a key model organism for studying the activity of interconnected brain circuits. A large scattered global research community of neurobiologists and neurogeneticists, computational and theoretical neuroscientists, and computer scientists and engineers has been developing a vast trove of experimental and modeling data that has yet to be distilled into new knowledge and understanding of the functional logic of the brain. Developing open shared models, modelling tools and data repositories that can be accessed from anywhere in the world is the necessary engine for accelerating our understanding of how the brain works.\n\nTo that end we developed the Fruit Fly Brain Observatory (FFBO), the next generation open-source platform to support open, collaborative Drosophila neuroscience research. FFBO provides a (i) hub for storing and integrating fruit fly brain research data from multiple data sources worldwide, (ii) unified repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease, and (iii) an open framework for fruit fly brain data processing and model execution. FFBO provides access to application tools for visualizing, configuring, simulating and analyzing computational models of brain circuits of the (i) cell type map, (ii) connectome, (iii) synaptome, and (iv) activity map using intuitive queries in plain English. Tools are provided to extract the function inherent in these structural maps. All applications can be accessed with any modern browser.

neuroscience↗

Visualization of axonal protein allocation in Drosophila with whole brain localization microscopy

Long-term memory (LTM) formation requires learning-induced protein synthesis in specific neurons and synapses within a neural circuit. Precisely how neural activity allocates new proteins to specific synaptic ensembles, however, remains unknown. We developed a deep-tissue super-resolution imaging tool suitable for single-molecule localization in intact adult Drosophila brain, and focused on the axonal protein allocation in mushroom body (MB), a central neuronal structure involved in olfactory memory formation. We found that insufficient training suppresses LTM formation by inducing the synthesis of vesicular monoamine transporter (VMAT) proteins within a dorsal paired medial (DPM) neuron, which innervates all axonal lobes of the MB. Surprisingly, using our localization microscopy, we found that these learning-induced proteins are distributed only in a subset of DPM axons in specific sectors along the MB lobes. This neural architecture suggests that sector-specific modulation of neural activity from MB neurons gates consolidation of early transient memory into LTM.

neuroscience↗

Asymmetric ephaptic inhibition between compartmentalized olfactory receptor neurons

In the Drosophila antenna, different subtypes of olfactory receptor neurons (ORNs) housed in the same sensory hair (sensillum) can inhibit each other non-synaptically. However, the mechanisms underlying this unusual form of lateral inhibition remain unclear. Here we use recordings from pairs of sensilla impaled by the same tungsten electrode to prove that direct electrical (\"ephaptic\") interactions mediate lateral inhibition between ORNs. Intriguingly, within individual sensilla, we find that ephaptic lateral inhibition is asymmetric such that one ORN exerts greater influence onto its neighbor. Serial block-face scanning electron microscopy of genetically identified ORNs and circuit modeling indicate that asymmetric lateral inhibition reflects a surprisingly simple mechanism: the physically larger ORN in a pair corresponds to the dominant neuron in ephaptic interactions. Thus, morphometric differences between compartmentalized ORNs account for highly specialized inhibitory interactions that govern information processing at the earliest stages of olfactory coding.

neuroscience↗

A single-cell level and connectome-derived computational model of the Drosophila brain

Computer simulations play an important role in testing hypotheses, integrating knowledge, and providing predictions of neural circuit functions. While considerable effort has been dedicated into simulating primate or rodent brains, the fruit fly (Drosophila melanogaster) is becoming a promising model animal in computational neuroscience for its small brain size, complex cognitive behavior, and abundancy of data available from genes to circuits. Moreover, several Drosophila connectome projects have generated a large number of neuronal images that account for a significant portion of the brain, making a systematic investigation of the whole brain circuit possible. Supported by FlyCircuit (http://www.flycircuit.tw), one of the largest Drosophila neuron image databases, we began a long-term project with the goal to construct a whole-brain spiking network model of the Drosophila brain. In this paper, we report the outcome of the first phase of the project. We developed the Flysim platform, which 1) identifies the polarity of each neuron arbor, 2) predicts connections between neurons, 3) translates morphology data from the database into physiology parameters for computational modeling, 4) reconstructs a brain-wide network model, which consists of 20,089 neurons and 1,044,020 synapses, and 5) performs computer simulations of the resting state. We compared the reconstructed brain network with a randomized brain network by shuffling the connections of each neuron. We found that the reconstructed brain can be easily stabilized by implementing synaptic short-term depression, while the randomized one exhibited seizure-like firing activity under the same treatment. Furthermore, the reconstructed Drosophila brain was structurally and dynamically more diverse than the randomized one and exhibited both Poisson-like and patterned firing activities. Despite being at its early stage of development, this single-cell level brain model allows us to study some of the fundamental properties of neural networks including network balance, critical behavior, long-term stability, and plasticity.

bioinformatics↗

Whole-brain imaging and characterization of Drosophila brains based on one-, two-, and three-photon excitations

To study functional connectome, optical microscopy provides the advantages of in vivo observation, molecular specificity, high-speed acquisition, and sub-micrometer spatial resolution. Now, the most complete single-neuron-based anatomical connectome is built upon Drosophila; thus it will be a milestone to achieve whole-brain observation with sub-cellular resolution in living Drosophila. Surprisingly, two-photon microscopy cannot penetrate through the 200-m-thick brain, due to the extraordinarily strong aberration/scattering from tracheae. Here we achieve whole-Drosophila-brain observation by degassing the brain or by using three-photon microscopy at 1300-nm, while only the latter provides in vivo feasibility, reduced aberration/scattering and exceptional optical sectioning capability. Furthermore, by comparing one-photon (488-nm), two-photon (920-nm), and three-photon (1300-nm) excitations in the brain, we not only demonstrate first quantitative reduction of both scattering and aberration in trachea-filled tissues, but unravel that the contribution of aberration exceeds scattering at long wavelengths. Our work paves the way toward constructing functional connectome in a living Drosophila.

neuroscience↗

The Fruit Fly Brain Observatory: from structure to function

The Fruit Fly Brain Observatory (FFBO) is a collaborative effort between experimentalists, theorists and computational neuroscientists at Columbia University, National Tsing Hua University and Sheffield University with the goal to (i) create an open platform for the emulation and biological validation of fruit fly brain models in health and disease, (ii) standardize tools and methods for graphical rendering, representation and manipulation of brain circuits, (iii) standardize tools for representation of fruit fly brain data and its abstractions and support for natural language queries, (iv) create a focus for the neuroscience community with interests in the fruit fly brain and encourage the sharing of fruit fly brain structural data and executable code worldwide. NeuroNLP and NeuroGFX, two key FFBO applications, aim to address two major challenges, respectively: i) seamlessly integrate structural and genetic data from multiple sources that can be intuitively queried, effectively visualized and extensively manipulated, ii) devise executable brain circuit models anchored in structural data for understanding and developing novel hypotheses about brain function. NeuroNLP enables researchers to use plain English (or other languages) to probe biological data that are integrated into a novel database system, called NeuroArch, that we developed for integrating biological and abstract data models of the fruit fly brain. With powerful 3D graphical visualization, NeuroNLP presents a highly accessible portal for the fruit fly brain data. NeuroGFX provides users highly intuitive tools to execute neural circuit models with Neurokernel, an open-source platform for emulating the fruit fly brain, with full data support from the NeuroArch database and visualization support from an interactive graphical interface. Brain circuits can be configured with high flexibility and investigated on multiple levels, e.g., whole brain, neuropil, and local circuit levels. The FFBO is publicly available and accessible at http://fruitflybrain.org from any modern web browsers, including those running on smartphones.

neuroscience↗

NeuroNLP: a natural language portal for aggregated fruit fly brain data

NeuroNLP, is a key application on the Fruit Fly Brain Observatory platform (FFBO, http://fruitflybrain.org), that provides a modern web-based portal for navigating fruit fly brain circuit data. Increases in the availability and scale of fruit fly connectome data, demand new, scalable and accessible methods to facilitate investigation into the functions of the latest complex circuits being uncovered. NeuroNLP enables in-depth exploration and investigation of the structure of brain circuits, using intuitive natural language queries that are capable of revealing the latent structure and information, obscured due to expansive yet independent data sources. NeuroNLP is built on top of a database system call NeuroArch that codifies knowledge about the fruit fly brain circuits, spanning multiple sources. Users can probe biological circuits in the NeuroArch database with plain English queries, such as \"show glutamatergic local neurons in the left antennal lobe\" and \"show neurons with dendrites in the left mushroom body and axons in the fan-shaped body\". This simple yet powerful interface replaces the usual, cumbersome checkboxes and dropdown menus prevalent in todays neurobiological databases. Equipped with powerful 3D visualization, NeuroNLP standardizes tools and methods for graphical rendering, representation, and manipulation of brain circuits, while integrating with existing databases such as the FlyCircuit. The userfriendly graphical user interface complements the natural language queries with additional controls for exploring the connectivity of neurons and neural circuits. Designed with an open-source, modular structure, it is highly scalable/flexible/extensible to additional databases or to switch between databases and supports the creation of additional parsers for other languages. By supporting access through a web browser from any modern laptop or smartphone, NeuroNLP significantly increases the accessibility of fruit fly brain data and improves the impact of the data in both scientific and educational exploration.

neuroscience↗