QI2 lab

mcSIM

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

OPM

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

I2K2022-SIM

I2K 2022 mcSIM tutorial

localize-psf

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

napari-spot-detection

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

Gpufit

GPU-accelerated Levenberg-Marquardt curve fitting in CUDA

napari-mcsim

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

sparse-deconv-py

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

SPIM_model

U-FISH

Deep learning based spot detection for FISH images.

2019-Kim-BiologyOpen

Image processing and analysis code for Kim et al 2019

cruzdb

python access to UCSC genomes database

merfish3d-analysis

3D MERFISH data processing

MVRegFus

Python module for registering and fusing multi-view microscopy data

napari-micromanager

npy2bdv

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

ProjectionSimulation

Simple simulation to compare standard and projection imaging

ray_trace_pb

Simple ray tracing in Python

rDL-SIM

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

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

IDT-using-Annular-Illumination

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

navigate

navigate - open source light-sheet microscope controls

pycrofluidics

A Python module for controlling Elveflow microfluidic devices