Journal Articles

• C. J. Gillon, C. Baker, R. Ly, E. Balzani, B. W. Brunton, M. Schottdorf, S. Ghosh, and N. Dehghani (2025). Open data in neurophysiology: Advancements, solutions & challenges. eNeuro, vol. 12, no. 11. DOI



Review article summarizing the current state of open data sharing in the field of neurophysiology as portrayed by the myriad of presentations and ensuing discussions from the inaugural Open Data in Neuroscience (ODIN) conference at MIT in 2023.

• data Open Data data Data Sharing

• K. Gunalan, R. Choudhury, et al. (2025). DANDI: Shaping the future of neurophysiology and neuroimage data publishing and exploration through collaboration with the community, standards, and analytic platforms. In preparation.



An in-progress manuscript detailing the cloud architecture, core features, and future plans for the DANDI archive for neurophysiology and neuroimaging data. Includes contributions from the entire extended DANDI team (10+ authors).

• archives DANDI data Data Standards data Data Sharing computing Cloud Computing

• R. Ly, C. Baker, S. Prince, and O. Rübel (2025). A practical evaluation of remote access methods for neurophysiology data in the cloud. In preparation.



An in-progress manuscript detailing a series of benchmarks which evaluate the performance of various remote access methods for reading data stored in AWS S3 cloud storage across a range of environmental and machine configurations.

• engineering Benchmarking computing AWS

• H. Mayorquin, C. Baker, P. Adkisson-Floro, S. Weigl, A. Trappani, L. Tauffer, O. Rübel, and B. Dichter (2025). NeuroConv: Streamlining neurophysiology data conversion to the NWB standard. Python in Science Conference, 2025. DOI



The seminal article presented at the SciPy conference which describes the years-long effort of creating NeuroConv, the automated data conversion tool capable of translating more than 40 distinct data formats used by neurophysiology acquisition devices to the NWB standard.

• Featured software

  NeuroConv

• standards NWB data Data Conversion languages Python

• J. Magland, J. Soules, C. Baker, and B. Dichter (2024). Neurosift: DANDI exploration and NWB visualization in the browser. Journal of Open Source Software, vol. 9, no. 97, p. 6590, 2024.

• Featured software

  Neurosift

• standards NWB archives DANDI analysis Data Visualization engineering Web Apps

• M. Hawrylycz, M. E. Martone, et al. (2023). A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS biology, vol. 21, no. 6, e3002133, 2023.



Consortium article (with dozens of authors) describing the data ecosystem developed by the BRAIN Initiative Cell Census Network, of which the DANDI Archive is a core component for data sharing and publication.

• archives DANDI archives BRAIN Initiative data Data Sharing

• C. Baker, E. Froudarakis, D. Yatsenko, A. S. Tolias, and R. Rosenbaum (2020). Inference of synaptic connectivity and external variability in neural microcircuits. Journal of Computational Neuroscience, vol. 48, pp. 123–147, 2020.



This paper made up the bulk of my doctoral thesis which explores the relationship between anatomical synaptic connectivity and observed spike train correlations in biophysically realistic systems of spiking neurons.

• neuroscience Computational Neuroscience neuroscience Spiking Neural Networks neuroscience Synaptic Connectivity neuroscience Correlations

• C. Baker, V. Zhu, and R. Rosenbaum (2020). Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance. PLoS computational biology, vol. 16, no. 9, e1008192, 2020.



This paper demonstrates how even simple biophysical plasticity rules can give rise to complex nonlinear computations in networks of spiking neurons operating within a semi-balanced regime. Trained a realistic spiking neural network in an unsupervised manner to perform image classification on the MNIST dataset.

• neuroscience Computational Neuroscience neuroscience Spiking Neural Networks neuroscience Balanced Networks neuroscience Synaptic Plasticity analysis Unsupervised Learning

• C. Baker, C. Ebsch, I. Lampl, and R. Rosenbaum (2019). Correlated states in balanced neuronal networks. Physical Review E, vol. 99, no. 5, p. 052 414, 2019.



My very first publication - mathematically derives the asymptotic scaling for spike count correlations in balanced networks of spiking neurons.

• neuroscience Computational Neuroscience neuroscience Spiking Neural Networks neuroscience Balanced Networks neuroscience Correlations

Conference Presentations

• C. Baker, G. Flynn, R. Ly, O. Rübel, and B. Dichter (2024). NWB GUIDE: Simplifying the conversion of neurophysiology data to NWB format. Society for Neuroscience (SfN) 2024.

• Featured software

  NWB GUIDE

• standards NWB data Data Conversion

• C. Baker, S. Weigl, H. Mayorquin, and B. Dichter (2023). NeuroConv: Automated conversion of neurophysiology data to NWB format. Society for Neuroscience (SfN) 2023.

• Featured software

  NeuroConv

• standards NWB data Data Conversion

• C. Baker, V. Zhu, and R. Rosenbaum (2020). Nonlinear computations in semi-balanced networks. Computational and Systems Neuroscience (COSYNE) 2020. Contributed talk (top 4% of abstracts).
• neuroscience Computational Neuroscience neuroscience Balanced Networks

• C. Baker and R. Rosenbaum (2018). Inferring connectivity and latent input covariance from spike train correlations. Computational and Systems Neuroscience (COSYNE) 2018. Poster (top 43% of abstracts).
• neuroscience Computational Neuroscience neuroscience Synaptic Connectivity neuroscience Correlations

Workshops

• C. Baker, R. Ly, and B. Dichter (2024). Neurodata Without Borders and DANDI Archive Tutorial. NWB and DANDI Workshop, Baylor College of Medicine.
• standards NWB archives DANDI

• C. Baker (2023). Neuroconv and NWB GUIDE tutorial. NWB User Days, Janelia Research Campus.

• Featured software

  NeuroConv NWB GUIDE

• standards NWB data Data Conversion

• C. Baker and R. Ly (2023). Neurodata Without Borders and DANDI Archive Tutorial. Pre-conference, COSYNE.
• standards NWB archives DANDI

• C. Baker, O. Rübel, and S. Ghosh (2023). Neurodata Without Borders and DANDI Archive Hackathon. NeuroDataShare, Sainsbury Wellcome Centre.
• standards NWB archives DANDI

• C. Baker and G. Viejo (2023). Artificial intelligence, machine learning, computing, and visualization in neuroinformatics. Open Data in Neuroscience (ODIN), Massachusetts Institute of Technology.
• data Open Data neuroscience Neuroinformatics analysis Data Visualization analysis Machine Learning

• C. Baker (2022). NeuroConv tutorial. NWB User Days, Janelia Research Campus.

• Featured software

  NeuroConv

• standards NWB data Data Conversion