Participant projects

A neurocentric account for context-dependent neural geometry

Zilu Liang, Mia Whitefield, Sumedha Nalluru

One of the core pursuits in neuroscience is to understand how information is encoded in neural activity.

Apply electrophysiological-based neuron classification methods to other dandisets

Stephanie Prince, Ambarish Ghatpande

Several approaches have been recently introduced to classify neurons by cell type based on electrophysiological data; we apply them to a new dandiset to test generalization across datasets.

Cyclic Adversarial Transformers for Temporally Stable Brain Computer Interface Decoding

Lyn Ackert-Smith

Creating robust BCIs is a challenge due to changing populations of neurons, but leveraging stable population dynamics can counteract this effect.

Generating Synthetic MRI Data Using GenAI Models to Enhance Neuroimaging Analyses

Reihaneh Hassanzadeh

This project utilizes generative AI to expand and enrich structural MRI datasets using a diffusion-based model.

Improving Low-Dimensional Embedding of Two-Photon Calcium Imaging Data Using Inferred Spiking Activity

Peter Hogg

Embedding tools like CEBRA can uncover low-dimensional representations of population activity that reflect task or stimulus related neural dynamics.

Mapping the brain across regions with single-unit activity

Cornelius Bergmann, Chris Halcrow, Mayo Faulkner, Ji Xia, Nisrine Bakri, Pierre Le Merre

In this project, we approached the organization of the brain at the level of single neuron activity.

Olfactory Representation in the Piriform Cortex

Nisrine Bakri

Understanding how odors are represented at the single-cell and population levels in the piriform cortex is key to deciphering olfactory perception.

Place field and oscillation changes with mouse kinematics

Yang-Sun Hwang, Eryn Sale

The hippocampus plays a critical role in spatial navigation and memory, but its representations are shaped by more than just the animal's location.

The relationship between neuromodulation and neurovascular coupling

Yunmiao Wang

This project explored spatiotemporal patterns in neurovascular data inspired by research on impulse response functions during spontaneous brain activity.

Whole-brain neuron-astrocyte information flow supporting futility-induced passivity

Marco Celotto, David Makoko, Camille Donoho, Ameyaltzin Castillo Almazán, Koray Cârsteanu, Cheng-Yu Huang

Mu et al. (2019) showed that norepinephrine-astrocyte signaling modulates neuronal activity to mediate futility-induced passivity in zebrafish.

Are cortical inhibitory neurons adjusting their cellular properties to local circuits?

Omar Valerio Minero

It is known that inhibitory neurons integrate into cortical circuits following the arrival of excitatory neurons.

Baseline Assessment of Cell Type Effects on Interpretable Neural Latent Dynamics

Keith Van Antwerp

How do opto-tagged cell types impact brain dynamics, using state-space modeling with a Poisson hidden Markov model as the baseline?

Building forecasting benchmarks for NeuroTask dataset

Carolina Filipe

Recent studies have shown that neural dynamics are preserved in animals performing different tasks, as well as in different animals performing the same task.

Comparison of spike sorting algorithms with SpikeInterface

Kate Doxey

Spike sorting is the process of extracting the activity of individual neurons from raw extracellular multi-electrode array recordings.

Dynamical modeling of decision-making through integrated behavioral and neural analysis

Luke Gong

Using dynamical systems to unravel the latent brain dynamics underlying decision-making processes.

Emotional and Cognitive Convergence during Naturalistic Movie Watching

Amber X. Chen

Investigate the impacts of emotional processing and cognitive engagement on memory retrieval, leveraging a multimodal dataset of single neuron, iEEG and fMRI data during movie watching and recall.

Estimating Partial Coherence Networks from Neural Spike Trains

Carla Pinkney

Statistically, neural spike trains can be represented by a multivariate point process whose second order structure can be characterised via the spectral density matrix.

Exploring Effective Pre-Training for Neuroscience Foundation Models with Neurodata Without Borders and DANDI

Yunlong Xu

Explore better pretraining tasks for foundation models in neuroscience, combining contrastive and masking pretraining on large-scale datasets.

Identification and distribution of prediction error-like signals in the mouse brain

Georg Raiser

Reward prediction error signals have classically been linked to dopaminergic neurons, but recent findings have uncovered similar signals from norepinephrine releasing neurons in the locus coeruleus.

Mapping spatial receptive fields in mouse visual cortex

Xinyue Ma

Benchmark methods for estimating spatial receptive fields from two-photon calcium imaging of visual cortical neurons.

Multiscale, Supervised Reanalysis of Optogenetically Induced Behavioral Reinforcement

Jack Goffinet

It has recently been shown that optogenetically evoked dopamine release in the dorsolateral striatum can reinforce the use of short behavioral syllables in the mouse.

Neural representation of ambiguity

Sophie Rogers

How does cue ambiguity impact the dynamics of choice formation across brain regions in the IBL Brain-wide Map dataset?

Pareto Optimality to Define the Topology of Brain States

Nils Nyberg

Leverage Pareto optimality to understand trade-offs in neuronal activity space.

Revisiting stability and plasticity in hippocampal sequence firing dynamics

Miles Martinez

Hippocampal place cells need to exhibit both stability and flexibility to support navigation through the world.

Smart neuromodulation approaches for motor control

Miguel Valencia

Developing smart electrical neuromodulation approaches for controlling motor disturbances related to Parkinson's disease.

Surface-based parcellation using high-resolution ex vivo 7 tesla MRI and microscopy imaging

Pulkit Khandelwal

MRI is the standard modality to understand human brain structure and function in vivo, and ex vivo imaging now opens the door to sub-millimeter study of brain structure.

The effect of probability on the structure of neural states

Yun Chen

Does the structure of preparatory neural subspaces in motor cortex geometrically represent reach in physical space, and does the probability distribution of targets change this map?

Understanding kinetics of neuropeptide release in presynaptic terminals

Luciana Gallo

CYbSEP is a novel tool to evaluate neuropeptide release by monitoring fusion of large dense-core vesicles.

Activity of single neurons during a declarative memory task

Fatmaalzahraa Aboalasaad

How the activity of single neurons during a declarative memory task (DANDI:000004) correlates with the encoding, retrieval, and consolidation processes of memory formation.

Analyzing spatiotemporal patterns from ECoG recordings

Tim Näher, Lisa Bastian

Analyze spatiotemporal patterns from ECoG recordings to identify patterns of neural activity in the sensorimotor cortex that correspond to different speech sounds and articulatory movements.

Bridging the gap between function and structure

Hannah Gooden, Victoria Rose, Daniel Xenes

Continued secondary analysis of the MICrONS dataset, including the two-photon calcium imaging hosted on the DANDI archive and the co-registered electron microscopy data hosted in the BossDB archive.

Contribution of physiological rhythms (respiration) to neural population geometries

Araceli Ramirez Cardenas

Disparities in parental response to visual and auditory cues from pups

Eberechi Wogu

Early maternal care is essential for the development and survival of offspring, and multiple sensory modalities such as visual, olfactory and auditory cues from the pups trigger parental responses.

IBL Brain-wide map: Adaptation and history biases across the brain hierarchy

Melanie Tschiersch

Analyze the IBL Brain-wide map to understand adaptation (repulsion from the previous stimulus) versus serial dependence (attraction to the previous stimulus) in visual processing versus higher-order cognitive areas.

Identifying homologies and diversifications of intrinsic physiological properties in rodents

Felipe Yáñez

Systematically assess the variability of intrinsic physiological properties of GABAergic interneurons across the cortical depth of rat barrel cortex and mouse visual and motor cortices.

Identifying latent states in decision-making tasks to uncover choice strategies

Zeinab Mohammadi

Rodent decision-making relies on distinct latent states which switch on a timescale of tens to hundreds of trials, and different brain regions' contributions to state-dependent strategies remain an important open problem.

Integrating Rule-Based Modulation and Context-Dependent Sensorimotor Adaptation in Cortical Areas

Tenghai Long

Explore the integration of rule-based modulation and context-dependent sensorimotor adaptation across cortical areas by analyzing electrophysiological data from DANDI:000239 and DANDI:000232.

Investigating neural representations of visual stimuli during encoding and retrieval

Sofia Raglio

Investigate how different the neural representation of visual stimuli in the medial temporal lobe is during encoding and retrieval.

Investigating the relationship between neuronal activity patterns and behavior in humans during decision-making tasks

Kshitij Kumar

Analyzing DANDI:000397 to investigate the relationship between neuronal activity patterns and behavior in humans during decision-making tasks.

Modulation of spontaneous neural activity by arousal

Martynas Dervinis

Neural activity can be broadly divided into fast and slow types; slow activity on the timescale of seconds is thought to underlie attentional processes and brain state transitions during wakefulness.

Neural trajectories in the anterior cingulate cortex during reward

Olivier Winter, Petrina Lau

Compute neural trajectories from raw AP data in the anterior cingulate cortex of the mouse around the reward event in the IBL task.

Neuronal ensembles in different brain regions

Ricardo Velázquez Contreras

Neuronal ensembles, as originally proposed by Donald Hebb, represent groups of neurons that display coordinated and alternating activity patterns.

Normative Models of Cognitive Representations

Will Dorrell

Testing normative theories of neural representation, which explain tuning curves as the optimum of a set of goals and constraints, against experimental data on DANDI.

Predicting cell type identity based on functional connectivity

Margaret Conde Paredes

Study task-specific neural trajectories and covariance in primate motor cortex electrophysiology data to gain insights into the neural mechanisms underlying motor control and movement generation.

The effect of different analysis techniques on the detection of fNIRS responses

Ishara Paranawithana

Investigate the impact of different analysis procedures on the morphology, detection, and lateralization of fNIRS responses in the motor cortex during a finger-tapping task (DANDI:000122).

Transcriptomic profiles and action potentials in GABAergic interneurons in the mouse visual cortex

Raymond L Wang

Understanding the relationship between transcriptomic profiles and action potentials in GABAergic interneurons in the mouse visual cortex using the Allen Institute Patch-seq dataset.

Constructing time-probability-matrices from simultaneously recorded visual areas using state space models

Brock Carlson, Blake Mitchell, David Zoltowski

Contrast sensitivity across layers and cell types within primary visual cortex

Blake Mitchell, Brock Carlson

To analyze V1 responses (2-photon calcium imaging) to full field images with varying image contrast.

Cross-Lab and Cross-Species co-clustering of cortical intracellular patch-clamp data

Sam Mestern

With this project, we aim to derive novel insights regarding cortical neuron differences between species and recording conditions.

Cross-species, cross-modality survey of bursting neurons

Chenggang Chen

Comparing the proportion of burst spiking neurons in the sensory cortex of non-human primates (macaque and marmoset) and rodents (gerbil and mouse).

Decoding history dependent neural activity in primary and higher visual areas

Lan Luo

Investigate how visual adaptation (history dependency of visual signals in the brain) transforms the encoding of stimulus identity using the Allen Institute Visual Behavior 2-Photon Imaging and Neuropixels datasets.

Elucidating Neural Learning Rules from Calcium Imaging Data

Felix Pei, Alessandro Salatiello

We want to analyze data from a mouse learning a task and see if any insight can be found regarding the learning rules used by the brain.

Ensemble computational models of neurons individually tuned with multimodal intracellular electrophysiology data

Krishna Pusuluri

Exploring the network of excitatory neurons with regularized GLMs

Tzu-Chi Yen, Yi-Yun, Josefina

This project explored statistical methods for extracting network structure from point process observations.

Feature-based embeddings of non-stationary ECoG

Brendan Harris

Describe the spatio-temporal dynamical structure of an ECoG recording using an existing pipeline for summarizing non-stationary neural data in a low-dimensional space of time-series features.

Finding neuronal networks based on shared temporal activity across task conditions

Noga Mudrik

A framework for finding interpretable functional neuronal networks presented across various non-stationary task conditions, and for assessing neural encoding uncertainty in the networks' latent space.

Fitting state space models in SSM repo to NWB datasets

David Zoltowski

My goal is to fit state space models in the SSM code package to NWB datasets.

Human iPSC-derived neurons recapitulate phenotypic variation within the human cortex

Michael Zabolocki

Human induced pluripotent stem cells (hiPSCs) offer a model which has the capacity to recapitulate the genetic underlying of the human brain across early neurodevelopment.

Identification of theta states in the prefrontal cortex

John Stout

Neural activity, paced at theta frequency (4-12 Hz) in the medial prefrontal cortex, is linked to memory-guided decision making.

Probing excitatory computations underlying probabilistic learning

Nuttida Rungratsameetaweemana

It is not well understood how excitatory and inhibitory neurons within each cortical region (as well as along the cortical hierarchy) work together to allow efficient information processing in dynamic environments.

Spyglass: data analysis framework for reproducible neuroscience research

Kyu Hyun Lee

Spyglass is a data analysis framework that brings together many open source tools, such as NWB, DataJoint, SpikeInterface, and others.

Sub-seconds Neural Emotion-Coding in Amygdala under Diverse Hippocampal Theta-Gamma States

Lu Zhang

How hippocampal theta-gamma coupling states affect neural emotion-coding in the amygdala, a brain region highly interacting with the hippocampus during emotion memory consolidation.

Using DANDI open datasets in transfer learning for decoding proprioception from neuronal calcium image using artificial neural network

Seungbin Park

Decoding proprioception is necessary for proprioceptive feedback to brain-machine interface to improve its movement performance.

Validating latent variable models in dandisets with rich behavioral data

Ben Lansdell

Tracking behavioral data from freely behaving animals, possibly in conjunction with neural recordings, is an exciting and growing direction in neuroscience.