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2019-kim-biologyopen

Image processing and analysis code for Kim et al 2019

cruzdb

python access to UCSC genomes database

gpufit

GPU-accelerated Levenberg-Marquardt curve fitting in CUDA

i2k2022-sim

I2K 2022 mcSIM tutorial

idt-using-annular-illumination

This is the MATLAB Implementation for Annular Illumination Intensity Diffraction Tomography (aIDT).

localize-psf

Code for localizing diffraction limited fluorescent objects and fitting the results to various different point-spread function (PSF) models.

mcsim

Code for running a multicolor structured illumination microscopy (SIM) experiment using a DLP6500 digital micromirror device (DMD) and performing SIM reconstruction.

mvregfus

Python module for registering and fusing multi-view microscopy data

napari-mcsim

Napari plugin automating structured illumination microscopy (SIM) reconstruction and diagnostics from the mcSIM package

napari-micromanager

napari-spot-detection

Detect diffraction limited spots in 2D and 3D, in standard or skewed microscopy images.

npy2bdv

Fast writing of numpy 3d-arrays into HDF5 and N5 Fiji/BigDataViewer files.

opm

Control, reconstruction, and analysis code for oblique plane microscopy.

projectionsimulation

Simple simulation to compare standard and projection imaging

ray_trace_pb

rdl-sim

A Tensorflow implementation of rationalized deep learning (rDL) based image denoising for microscopy images

sparse-deconv-py

Official Python implementation of the 'Sparse deconvolution'-v0.3.0

spots3d

GPU accelerated spot finding and localization for both skewed (diSPIM, lattice, OPM) and standard geometry (widefield, confocal) 3D microscopy data.

storm-control

Microscope control software