Available implementations

This page references smart-microscopy implementations for different manufacturers and academic labs. We highly encourage community contributions, contact us or add your entry via the GitHub repository!

Academic implementations

Project overview	Repo	Institution	Contact
rtm-pymmcore: Automated optogenetic targeting	pertzlab/rtm-pymmcore	UNIBE	Lucien Hinderling
Outcome-driven microscopy to guide cell biology	UU-cellbiology/UU_SmartMicroscopy	UU	Alfredo Rates
Modular adaptive feedback microscopy workflows with AutoMicTools	git.embl.de/halavaty/AutoMicTools	EMBL-ALMF	Aliaksandr Halavatyi
Smart Microscopy as a Service		CCI-UG	Rafael Camacho
CelFDrive: Multimodal AI-Assisted Microscopy for Detection of Rare Events	scott-vision/CelFDrive	UoW, 3i	Scott Brooks
The EnderScope as an educational platform for Smart Microscopy	mutterer/enderscopy	CNRS	Jerome Mutterer
PyCLM: programming-free, closed-loop microscopy for real-time measurement, segmentation, and optogenetic stimulation	Harrison-Oatman/PyCLM	Princeton	Jared Toettcher

Industry implementations

Product overview	Repo	Brand	Contact
Inscoper’s Roboscope		Inscoper	Otmane Bouchareb
Open Application Development (OAD) in Zeiss ZEN	zeiss-microscopy/OAD	ZEISS	Philipp Seidel
ImSwitch for openUC2	openUC2/imswitch	openUC2	Benedict Diederich
	Luxendo/Acquifer-Python-API	LUXENDO	Thomas Laurent
Automation of single-cell analysis with Cytely		Cytely	Karl Johansson
Visual programming for Smart Microscopy with NIS-Elements (Nikon)	Customer E-learning	Nikon	Andrii Rogov

Hardware / Software compatibility

These tables provide a more general overview, also linking to projectes not yet represented in the working group. An overview of relevant software can also be found here: https://smartmicroscopy.org/resources/

Hardware compatibility matrix

Brand	Internal scripting support	Interoperable external software	API	Open source compatibility	Examples provided	Licence free of charge
Acquifer IM	✓	✓	✓	Medium	Prescreen - rescreen	✓
Evident (formely Olympus)	✓	✓	✓	Medium	✓	✕
Inscoper	✕	✓	✓	High	✓	✕
Leica	✓	✕	✕	Low	✕	✕
Viventis	✕	✓	✓	Medium	✓	✓
Luxendo	✕	✓	✕	Medium	✓	✓
Nikon	✓	✓	✓	Medium	Scheduler API	✕
openUC2	✓	✓	✓	High	✓	✓
Zeiss	✓	✓	✓	Medium	OAD TCP-IP interface	✕
PicoQuant MicroTime 200	✓	✓	✕	High (via TCP/IP)	✓ (not public)	✕
RAPP OptoElectronic	✕	✓	✓	High	✕	✕

Software compatibility matrix

Software	License	GUI / Coding	Compatible hardware	Repo	Publication
Zeiss Zen OAD	Commercial	API	Zeiss LM microscopes	zeiss-microscopy/OAD
Nikon NIS-Elements Jobs module / macro language	Commercial	GUI and API	Nikon microscopes
Leica LAS-X	Commercial	GUI	Leica microscopes
Inscoper	Commercial	GUI and API	Devices supported by Inscoper
SymPhoTime64	Commercial	API	PicoQuant MicroTime200
Cytely	Commercial	GUI	Nikon: full support, other devices: partial support		link
Evident (formely Olympus) Macro to Micro	Commercial	GUI	Evident microscopes operated by cellSens
Evident (formely Olympus) RMTDK	Commercial	API	Evident Point scanning confocals
RAPP OptoElectronic - SysCon	Commercial	API	RAPP photomanipulation devices
AutoMicTools package	Open source	GUI and API	Several commercial microscope brands (e.g. Zeiss, Olympus/Evident, Nikon)	https://git.embl.de/halavaty/AutoMicTools
				https://git.embl.de/grp-almf/zeiss_zenblue_automation/
				https://git.embl.de/grp-almf/automictools-fluoview-bridge
pymmcore-plus	Open source	API	μManager devices & custom devices
pymmcore-gui	Open source	GUI	GUI for pymmcore-plus backend	pymmcore-plus/pymmcore-gui
pymmcore-widgets	Open source	GUI	GUI for pymmcore-plus backend	pymmcore-plus/pymmcore-widgets
napari-micromanager	Open source	GUI	GUI for pymmcore-plus backend	pymmcore-plus/napari-micromanager
pymmcore-eda	Open source	API	Dynamic acquisitions using pymmcore-plus backend	LEB-EPFL/pymmcore-eda	link
rtm-pymmcore	Open source	API	Adaptive photomanipulation using pymmcore-plus backend	pertzlab/rtm-pymmcore
Navigate	Open source	GUI and API	μManager devices and custom devices		link
ImSwitch	Open source	GUI and API	μManager devices, wide range of devices via python, openUC2	openuc2/ImSwitch	link
Pycro-Manager	Open source	API	μManager devices & custom devices	micro-manager/pycro-manager	link
AutoPilot	Open source	API	Custom built	MicroscopeAutoPilot/autopilot	link
AutoScanJ	Open source	API	Leica LAS AF/X and μManager devices		link
MicroMator	Open source	GUI and API	μManager devices	Gitlab	link
CyberSco.Py	Open source	GUI and API	XCite LED and Andor camera	Lab513/CyberSco.Py	link
Microscopy Pipeline Constructor (MyPiC)	Open source	API	Zeiss LSM780 / LSM880	manerotoni/mypic	link
Adaptive Feedback Microscopy ImageJ/FiJi utilities	Open source	API	Enabling adaptive feedback microscopy with MyPiC backend	https://git.embl.org/grp-ellenberg/adaptive_feedback_mic_fiji	link