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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.

fast-bonito

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"

metalens

Design, optimize, & simulate metasurface lenses (aka diffractive lenses), beam deflectors, gratings etc

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