Computational Microscopy Platform (Mehta Lab), CZ Biohub

microDL

3D virtual staining with 2D and 2.5D U-Nets

microlith

Image simulation for microscopy and lithography systems

VisCy

computer vision models for single-cell phenotyping

dynamorph

Learn morphological states of dynamic cells

waveorder

Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.

recOrder

3D quantitative label-free imaging with phase and polarization

reconstruct-order

Label-free measurement of density and anisotropy from polarization-resolved images

dynacontrast

Image-based phenotyping of single cells using self-supervised contrastive learning

multiSero

serological measurements from multiplexed ELISA assays

MM_meadowlarkLC_opensource

Open source micro-manager adapter for Meadowlark Liquid Crystal controllers.

instantPolScope-matlab

Imaging molecular order in live cells using fluorescence polarization.

miPolScope

miPolScope: rapid label-free imaging across wavelegnths

.github

AcqEngJ

Java-based acquisition engine for Micro-manager

aicsimageio

Delayed Parallel Image Reading for Microscopy Images in Python

micro-manager

Microscope control and image acquisition integrated with ImageJ.

micro-manager.github.io

Micro-Manager website source

mmCoreAndDevices

Micro-Manager's device control layer, written in C++

napari-allencell-segmenter

A plugin that enables image segmentation provided by Allen Institute for Cell Science

napari-glyphs

NDTiffStorage

N-dimensional, multiresolution file format for Micro-Manager

NDViewer

N-D multichannel multiresolution image viewer for Micro-Manager

octopi-research

pycro-manager

Python control of micro-manager for customized data acquisition

tensor-visualization

Visualization of uniaxial permittivity tensors measured with polarization microscopy in 2D and 3D space

TriggerScopeMM

Micro-Manager-specific firmware for the TriggerScope