Featured senior project

Morphological Determinants of Neuronal Excitability

Planned senior-year project integrating NeuroMorpho.org neuronal reconstructions, Allen Institute Cell Types morphology and electrophysiology data, and NEURON simulations to study how neuronal structure relates to excitability.

NeuroMorpho.org Allen Institute NEURON SWC morphology
Featured planned senior project

Morphological Determinants of Neuronal Excitability

A planned senior-year project connecting morphology curation, public Allen Institute cell data, and NEURON simulations into one computational neuroscience portfolio piece.

NeuroMorpho.org Allen Institute NEURON SWC morphology
Data source NeuroMorpho.org reconstructions
Comparison Allen Institute cell morphology and physiology
Modeling NEURON simulations of excitability
Research profile

NeuroMorpho.org Research Assistant

I support NeuroMorpho.org through literature mining and neuroinformatics data curation for digitally reconstructed neurons and glia, with emphasis on reconstruction evidence, tracing methods, metadata quality, and data-source availability.

01

Reconstruction Evidence

Evaluated scientific articles for evidence of bifurcating, skeletonized neuronal or glial reconstructions. Identified reconstruction and tracing methods including Neurolucida, Imaris Filament Tracer, Amira, Vaa3D, Simple Neurite Tracer, and related tools.

02

Literature and Data Review

Reviewed figures, captions, supplementary materials, data availability statements, and repository links to determine whether reconstruction data were accessible. Classified articles as positive, negative, inaccessible, or shared-source based on reconstruction evidence and metadata standards.

03

Metadata Curation

Documented reconstruction details, tracing methods, confidence levels, DOI/PMID links, author information, and data-source availability. Developed experience with neuroscience metadata curation, morphology-focused literature review, scientific data provenance, and quality control for large-scale neuroinformatics resources.

Selected work

Selected computational neuroscience work.

The project section emphasizes work that supports my target direction: computational neuroscience, scientific data analysis, NEURON modeling, and neuroinformatics.

Featured planned senior project

Morphological Determinants of Neuronal Excitability

Planned senior-year project integrating NeuroMorpho.org neuronal reconstructions, Allen Institute Cell Types morphology and electrophysiology data, and NEURON simulations to study how neuronal structure relates to excitability.

NeuroMorpho.org Allen Institute NEURON SWC morphology
Project

Hodgkin-Huxley Neuron Simulator

Built a biophysical neuron simulator using the Hodgkin-Huxley mathematical framework, investigated how sodium and potassium conductance parameters shape spike behavior, and validated outputs against NEURON for numerical and biological realism.

Computational neuroscience Neuron modeling NEURON validation
Planned

NEURON Simulator GUI Single Cell Model

NEURON GUI Single-cell model
Planned

NEURON Simulator Python Scripted Single Cell Model

NEURON Python Single-cell model
Planned

NEURON Simulator Python Scripted Neuronal Circuit Model

NEURON Python Circuit model
Coursework

Relevant academic preparation.

A neuroscience foundation with increasing emphasis on data mining, computational modeling, and neuroinformatics.

Neuroscience

  • NEUR 327Cellular NeuroscienceGrade received: A
  • NEUR 328Cellular Neuroscience LabGrade received: B
  • NEUR 335Developmental and Systems NeurosciencePlanned
  • NEUR 430Computational NeurosciencePlanned
  • NEUR 431NeuroinformaticsPlanned
  • NEUR 471The Changing Brain: Evolution and DevelopmentPlanned
  • NEUR 473Current Neuroscience Research in Germany
  • PSYC 375Brain and Sensory ProcessesGrade received: A
  • PSYC 376Brain and BehaviorPlanned
  • PSYC 373Biopsychology LabPlanned

Engineering and Data

  • BENG 434Computational Modeling of Neurons and NetworksPlanned
  • CDS 303Scientific Data MiningPlanned
  • BENG 499Special Topics in Bioengineering
  • ENGR 107Introduction to Engineering

Biology, Math, and Physics

  • BIOL 213Cell Structure and Function
  • BIOL 214Biostatistics for Biology Majors
  • BIOL 311General Genetics
  • MATH 113Analytic Geometry and Calculus I
  • PHYS 160University Physics I
Contact

Open to research and technical opportunities.

I am interested in computational neuroscience, neuroinformatics, morphology data, scientific data curation, and neuroscience modeling roles.

Preview of Nicholas Johnson resume
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