OM_Software.md
July 23, 2026 · View on GitHub
Open-microscopy software
Project | Description | Resources |
|---|---|---|
| ACCéNT | Plugin for Fiji and Micro-Manager which allows to calibrate the pixel-wise noise characteristics of (s)CMOS cameras from dark images alone. Ries Lab. | Diekmann2021, GitHub |
| autoFRET | An automated single-molecule FRET platform for multiwell-plate screening of biomolecular conformations and dynamics. Schlierf lab Lab. | Hartmann2023, GitHub |
| BactMap | R-based software to combine and analyse segmentation & fluorescence data derived from custom software like Oufti, Morphometrics, MicrobeJ or Supersegger. | Raaphorst2019, GitHub |
| BigDataViewer | Visualization and processing of large, multi-terabyte image datasets; a foundational viewer across the Fiji/ImgLib2 ecosystem. | Pietzsch2015, GitHub |
| BigStitcher | Reconstruction and stitching of high-resolution, multi-tile light-sheet and cleared/expanded sample datasets. | Hörl2019, GitHub |
| Biobeam | Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy (Python) | Weigert2018. GitHub |
| Bio Image Book | Introduction to Bioimage Analysis using Jupyter notebooks (Python) | Bankhead2022/GitHub |
| Bright-Eyes MCS | Software for real-time preview etc., support for SPAD arrays etc, storing in HDF5, works with SMLM / scanning modalities. | Donato2024, GitHub |
| CaImAn | Scalable toolbox for calcium-imaging analysis: motion correction, source extraction, spike deconvolution. | Giovannucci2019, GitHub |
| CARE | Denoising that enables low-photon dose imaging using neural networks. | Weigert2018. GitHub |
| Clij | GPU-accelerated image processing. | Haase2020 GitHub |
| Cellpose | Cell segmentation. | Stringer2021, GitHub |
| CellProfiler | Image Processing for high-throughput imaging. Carpenter lab. Version 3.0. | Website, McQuin2018 |
| Cluster analysis for SMLM data | Software packages for cluster identification and analysis by Owen lab | Rubin-Delanchy2015 |
| ColiCoords | Python-based software for creating a coordinate system in segmented rod-shaped cells for the alignment and aggregation of many cells. | Smit2019, GitHub |
| CSBdeep | Deep Learning platform for ImageJ/Fiji | Website |
| DECODE | Deep learning tool to fit high-density raw data in SMLM, based on Python and Pytorch. Macke, Ries and Turaga Labs. | Speiser2021, GitHub |
| Deconvolution and multiview | Rapid image deconvolution and multiview fusion for optical microscopy. Shroff lab. | Guo2020, GitHub |
| DeepCell / Mesmer | Deep-learning library for single-cell and whole-cell segmentation of tissue images. Van Valen lab. | Greenwald2022, GitHub |
| Deepthought | Repository for next generation microscope control software. Python. | IntroVideo, GitHub |
| DL4MicEverywhere | DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible. | Hidalgo-Cenalmor2024, GitHub |
| Eigenpsf-extractor | Extract PSFs from 2D and 3D images and estimate eigenpsf : a basis allowing you to represent PSFs compactly. | GitHub |
| EMU | Easier Micro-Manager User interface. Plugin for Micro-Manager allowing creation of versatile GUIs that can be easily adapted to control different devices and microscopes. Ries Lab. | Deschamps2020, GitHub |
| fairSIM | Open source SIM reconstruction. | Website, Müller2016, GitHub |
| Fiji | General-purpose image processing. Fiji is just ImageJ. | Schindelin2012, Website |
| FlexSIM | A flexible SIM reconstruction method capable to handle difficult data prone to reconstruction artifacts. | Soubies2024, GitHub |
| FluorescenceTools | A collection of GitHub repositories for open source fluorescence spectroscopy software. | Website |
| FRET community software list | A collection of software for the analysis of single-molecule FRET experiments of all kinds. | Website |
| GlobalBioIm | A unifying Matlab framework for the development of reconstruction algorithms in computational imaging. | Website, Soubies2019, GitHub |
| ilastik | Pixel and object classification using machine learning. | Berg2019, Website, GitHub |
| ImJoy | Browser- and plugin-based image processing and machine learning. Lundberg lab and Zimmer lab. | Ouyang2019, Website |
| ImSwitch | Python-based microscopy control software, Plug-and-Play. Testa lab. | CasasMoreno2021, GitHub |
| Inverse Modelling | All kinds of software projects that perform inverse modelling, deconvolution, lightfield microscopy, optical wave simulation, etc.; Code in Python, Matlab. Waller lab. | GitHub |
| Labthings | Internet-of-Things-based Hardware control (e.g. Microcontrolers) | GitHub |
| LIVECell | A large-scale dataset for label-free live cell segmentation. | Edlund2021 |
| localize-psf | Code for localizing diffraction limited fluorescent objects and fitting the results to various different point-spread function (PSF) models. This includes tools for doing localization on the GPU using a modified version of GPUfit. (Python) | GitHub |
| LocMoFit | LocMoFit is a framework to fit SMLM data with geometric models. It comes as a plugin of SMAP (see below). Ries Lab. | Wu2021, GitHub |
| MDEmic | A metadata annotation tool to facilitate management of FAIR image data in the bioimaging community. | Kunis2021, GitHub |
| micro-sam | Segment Anything adapted for microscopy: interactive and automatic segmentation and tracking across modalities. | Archit2025, GitHub |
| microEye | A python toolkit for data acquisition within one graphical user interface and accessing tiff images and perform localization analysis. It also allows for visualizing the filtering-localization process WYSIWYG. | GitHub |
| micromanager | Microscope-Control Software with a large user and hardware plugin community | Edelstein2010, Website |
| mcSIM | Code for designing, analyzing, and carrying out multicolor structured illumination microscopy experiments. Additional tools for digital micromirror device SIM (DMD-SIM), including DMD simulation code, DMD pattern generation, SIM reconstruction and instrument control. (Python and Java) | Brown2021, GitHub |
| MorphoLibJ | Integrated library and ImageJ/Fiji plugins for mathematical morphology — filtering, segmentation, measurements. | Legland2016, GitHub |
| Multi-view deconvolution | Real-time multi-view deconvolution for lightsheet microscopy. Huisken lab. | Schmid2015 |
| NanoImagingPack | Various functions to simulate optical imaging in microscopy; 3D, Polarization, Wave propagation, etc. Python | GitLab |
| NanoJ-SQUIRREL | Quantitative mapping and minimization of super-resolution optical imaging artifacts. | Culley2018, GitHub |
| Napari | nD Viewer for python, expendable using plugins | Website, GitHub |
| Noise2Void | Machine learning-based denoising without datasets. | Krull2019, GitHub |
| ODT-LS | Optical diffraction tomography reconstruction using Lippmann-Schwinger model. | Pham2020, GitHub |
| Omega | Omega — harnessing the power of large language models for bioimage analysis | Royer2024, GitHub |
| Omnipose | Morphology-independent deep-learning segmentation, robust for elongated and bacterial cells. | Cutler2022, GitHub |
| OpenFlexure Server | Internet-of-things based microscopy control (Raspberry Pi) | Website, GitLab |
| Open Microscopy Environment | Open Microscopy Environment, OME) is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. | Website |
| snouty-OPM | Control and analysis code for OPM using a solid immersion tertiary objective (aka Mr. Snouty). (Python and Java) | Sapoznik2020, GitHub |
| PAM | PIE analysis in MATLAB - Analysis software for point or image fluorescence experiments using pulsed-interleaved excitation. Single-molecule FRET, FCS, ICS, PhasorFLIM. | Schrimpf2018, Website |
| PERPL | Structure-based modelling of microscopy data | Curd2021, BitBucket |
| Picasso | Python-based analysis software for single-molecule localisation microscopy. Jungmann lab. | SchnitzbauerStrauss2017, GitHub |
| Phasor-based SMLM | Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): An algorithm for MHz localization rates using standard CPUs | Martens2017, GitHub |
| pycro-manager | Python-based Microscope-Control for micromanager. | Pinkard2021, GitHub |
| PyFocus | Python package for vectorial calculations of focused optical fields. | Caprile2021, GitHub |
| PyLabLib | PyLabLib cam-control: Software for universal camera control and frames acquisition. Sandoghdar lab. | GitHub |
| PYME | Python-based open-source tool for super-resolution microscopy and data. | Marin2021, GitHub |
| Python Microscope | Microscope is a Python package for the control of microscope devices. It is the fastest and easiest method to incorporate image analysis as part of a microscope experiment. | Website |
| Mars | Molecule archive suite is broad framework for image processing, storage and reproducible analysis of single-molecule data. | Website, GitHub |
| Microscope-Cockpit | An open-source approach for user friendly fully programmable bespoke microscopy (Micron, Oxford). | Website, GitHub |
| navigate | Open-source platform for smart light-sheet microscopy. Sheppard, Fiolka, Dean labs. | Marin2024, GitHub |
| Quantitative Phase Imaging Tools | Various Tools to reconstruct brightfield images under varying illumination using inverse modeling and neural networks. Datasets. Lei Tian Lab. | Website, GitHub |
| QuPath | Open software platform especially for histopathology. | Bankhead2017, GitHub, |
| Ray-optics web app | An open-source web application to simulate reflection and refraction of light. | GitHub/Website |
| SMAP | Open-source superresolution microscopy analysis platform. MATLAB-based tool with GUI to fit raw data, post-process and analyze SMLM data. Contains a powerful ROI manager and many other plugins, can be extended by own plugins (documentation available). Ries Lab. | Ries2020, GitHub |
| SNT | Fiji toolbox for reconstruction, quantification, and visualization of neuronal anatomy. | Arshadi2021, GitHub |
| Spotiflow | Accurate, robust deep-learning spot detection for fluorescence microscopy (FISH, single molecules). Weigert lab. | DominguezMantes2025, GitHub |
| StarDist | Nuclei segmentation. | Weigert2019, GitHub |
| suite2p | Pipeline for two-photon calcium imaging: registration, cell detection, and signal extraction. MouseLand. | Pachitariu2016, GitHub |
| ThunderSTORM | An open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods. | Ovesný2014, GitHub |
| ThunderSTORM Origami Analyzer | Automated DNA origami analysis of ThunderSTORM localization data and reconstruction of super-resolution images. | GitHub, Docs |
| TrackMate | Widely used Fiji platform for single-particle tracking, with pluggable detectors/segmentation and trackers. | Tinevez2017, Ershov2022, GitHub |
| Various | Zhao lab: sparsedeconvolution for image deconvolution, rFRCmetric for resolution/image-quality mapping, SN2N for image denoising: | GitHub |
| Wave Blocks | An open-source tool for inverse modelling modular optical system. Written in Tensorflow and supports deconvolution and arbitrarily complicated optical setups. Done with automatic differentiation | GitHub |
| webSMLM | A browser-based framework for single-molecule localisation microscopy (SMLM) featuring fast data processing, modern 3D drift correction and live rendering. | GitHub,Launch webSMLM |
| ZeroCostDL4Mic | Deep Learning accessible to microscopists by means of Google Colab Notebooks | Chamier2021, GitHub |