smeanapole's repositories
BerkeleyPhotonicInverseDesign
Continuous Adjoint Optimization with Lumerical, developed at UC Berkeley
compressive-sensing-Gerchberg-Saxton
Software implementation of multiple algorithms for the generation of 3D optogenetics photostimulation patterns with phase-only spatial light modulators
DataAcquisition
MATLAB graphical user interface for viewing and recording data using a National Instruments DAQ, tested specifically for the NI USB-6003.
hedges
HEDGES Error Correcting Code for DNA
HMM
Hidden Markov models for biological time-series data, implemented from scratch in Matlab
jetson_nanopore_sequencing
A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
LDPC_DNA_storage
LDPC codes for Illumina sequencing-based DNA storage
MagneticTweezers
A single-molecule manipulation instruments that utilize a magnetic field to apply force to a biomolecule-tethered magnetic bead.
master_of_pores
Nextflow pipeline for analysis of direct RNA Nanopore reads
matplotlib_for_papers
Handout for the tutorial "Creating publication-quality figures with matplotlib"
Multiple-constrained-phase-retrieval
This repository contains a solution to multiple constrained phase retrieval problem.
nanocompore_paper_analyses
Analyses performed for the nanocompore paper
nanopolish_mRNA-1273
Nanopolish polya-moderna for the identification of terminal pentamer in the mRNA-1273 direct RNA sequencing data
Nanopore
MRes Research Project
NanoporeCode
Code to analyze nanopore data in the Golovchenko lab.
NanoSim
Nanopore sequence read simulator
objective-first
Objective-first approach to nanophotonic design, implemented in Matlab
picasso
A collection of tools for painting super-resolution images
PiSCAT
PiSCAT is a python-based package with a graphical user interface for performing high-performance analysis on a variety of iSCAT measurements.
Porcupine
Porcupine is a molecular tagging system to tag physical objects with DNA.
read_until_api_v2
Python3 Read Until API implementation
readfish
Read Until scripts
SLM-3dPointCloud
Python library for generating 3d point cloud holograms, with phase only spatial light modulators, in real time through a GPU implementation of 5 algorithms (Random superposition, Gerchberg-Saxton, weighted Gerchberg-Saxton, compressed sensing Gerchberg-Saxton, compressed sensing weighted Gerchberg-Saxton).
spins-b
Photonic optimization library
SquiggleKit
SquiggleKit: A toolkit for manipulating nanopore signal data
stepfinder
Stepfinder: A Python package to find steps in one dimensional data with low SNR
tidy3d-notebooks
Collection of examples and tutorials for the Tidy3D solver by Flexcompute Inc
UNCALLED
Raw nanopore signal mapper that enables real-time targeted sequencing
VideoMetamaterials
Implementation of 'Inverse-design of nonlinear mechanical metamaterials via video denoising diffusion models'