Computational Cognitive Neuroscience textbook

A python package for simulating motion in continuous environments and spatial cell types (e.g. place cell).

3D-UCaps: 3D Capsules Unet for Volumetric Image Segmentation (MICCAI 2021)

State space models for decoding hippocampal trajectories and determining their type using sorted or clusterless data

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

In this project I develop a deep learning CNN model to predict Alzheimer's disease using 3D MRI medical images of the Hippocampus region of the brain.

AICONSlab's hippocampal segmentation algorithm using CNNs

Axon is a spiking, biologically-based neural model driven by predictive error-driven learning, for systems-level models of the brain

State space models for categorization of replay content from multiunit spiking activity. Deng et al. 2016

Deep spectral-based shape features for Alzheimer’s Disease classification

Code for analysis on data from Jadhav et al. 2016

Partial analyses to accompany "Uncovering temporal structure in hippocampal output patterns".

Built an end-to-end AI system which features a deep learning algorithm that integrates into a clinical-grade viewer and automatically measures hippocampal volumes of new patients, as their studies are committed to the clinical imaging archive.

Hippocampal Segmentation Factory (HSF). A one-liner Deep Learning tool to segment raw T2w (and T1w) MRIs into hippocampal subfields in few seconds. Trained on 700+ manually segmented hippocampi.

A semi-latent state-space model that combines movement, LFP, and ensemble spiking information to identify periods of replay and decode its content in real time. Long Tao et al., unpublished.

Application of AI in 3D Medical Imaging in quantifying Alzheimer's disease progression through automated measurement of hippocampal volume

This detailed and robust compartmental model accompanies the manuscript Beining et al (2017): T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells. eLife

Full-scale biophysical model of the dentate gyrus

Hippocampal transcriptomic responses to enzyme‐mediated cellular dissociation

Python script & library to read hippocampal volumes computed by Freesurfer & ASHS