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Welcome to cechava's Github! 👋

I'm a Computational Neuroscientist with an enthusiasm for extracting insights from behavioral, physiological, and image data.

This github page cotains some of the work I have done during my time in neuroscience research at Harvard and MIT as well as some other portfolio projects. Here are some of my favorite projects:

  • Rectilinearity-Toolbox, a MATLAB-based image processing package to quantify the amount of rectilinear (right-angle) features in an image. I used this package to contribute to a neuroscience journal publication showing that a region of the brain is particularly sensitive to the presence of rectilinear features which are ubiquitous in natural and man-made enviroments.
  • simple-eyetracker A simple semi-supervised Python-based eye tracking software I developed to keep track of animal pupil dilation and eye movements in brain physiology experiments.
  • EMG-gestures A deep learning-based package to decode hand gestures from electrical signals in the forearm (electromyography - EMG). The package also benchmarks different strategies for transferring learned callibrations across subjects.

cechava's Projects

badges icon badges

:pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yours!

ca_source_extraction icon ca_source_extraction

Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.

deeplabcut icon deeplabcut

Markerless tracking of user-defined features with deep learning

extract-public icon extract-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.

facemap icon facemap

matlab GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)

gcamp icon gcamp

analysis scripts for GCaMP data

hdmf icon hdmf

The Hierarchical Data Modeling Framework

helperfunctions icon helperfunctions

Common functions that may be used by all other functions in the Harvey Lab code base.

matnwb icon matnwb

A Matlab interface for reading and writing NWB files

normcorre icon normcorre

Matlab routines for online non-rigid motion correction of calcium imaging data

pynwb icon pynwb

A Python API for working with Neurodata stored in the NWB Format

roiextractors icon roiextractors

Python-based module for extracting from, converting between, and handling recorded and optical imaging data from several file format. Inspired by SpikeExtractor

suite2p icon suite2p

cell detection in calcium imaging recordings

tf-dann icon tf-dann

Domain-Adversarial Neural Network in Tensorflow

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