🟤Bioimaging Viewers

Open-Source Bioimage Viewers

Here is a list of Open-source viewers best suited for life-science microscopy (fluorescence/confocal/spinning-disk, widefield, light-sheet, live-cell, EM/WSI).

Name	Platform (OS)	Primary modalities	N-D support (C/Z/T)	File format backbone	Notable limitations / caveats
Fiji (ImageJ)	Desktop (Win/macOS/Linux)	Widefield, confocal, light-sheet, EM; everything from single fields to mosaics	2D–5D (C/Z/T)	Bio-Formats, OME-TIFF	Performance on very large datasets needs care (RAM, tiling); UI can feel legacy; plugin quality varies
napari	Desktop (Win/macOS/Linux; Python)	Fluorescence/confocal/light-sheet; interactive labeling/annotation; N-D arrays	2D–5D	Readers for OME-TIFF, Zarr, and many plugins	Ecosystem still maturing in some niches; requires Python setup for best use
Icy	Desktop (Win/macOS/Linux)	Fluorescence/confocal/time-lapse; interactive workflows	2D–4D	Bio-Formats, TIFF/OME-TIFF	Smaller ecosystem vs Fiji/napari; fewer cutting-edge big-data tools
QuPath	Desktop (Win/macOS/Linux)	Brightfield/IF pathology, WSI; tiles & tissue slides	2D (multi-channel)	Bio-Formats; pyramidal WSI formats; OME-TIFF	Primarily 2D WSI (less for Z/T stacks); microscopy timelapse/volumetric less central
OMERO.iviewer	Web (server-backed: OMERO)	Lab microscopy across modalities; central data portal	2D–5D	OME stack via OMERO	Requires OMERO server; analysis is limited vs desktop tools
BigDataViewer (Fiji plugin)	Desktop (Java; via Fiji)	Light-sheet, large 3D volumes, multi-view	3D/4D/5D	HDF5/N5; OME-TIFF via bridges	Viewer/IO focused; relies on Fiji for processing; learning curve
MoBIE (Fiji-based)	Desktop (Fiji plugin)	Cell/EM/light-sheet atlases; multi-modal big data	3D/4D/5D	N5/Zarr, OME-TIFF	Project structure conventions; best when adopting N5/Zarr
ilastik	Desktop (Win/macOS/Linux)	Fluorescence/confocal; interactive pixel/object classification, tracking	2D–4D	Bio-Formats, TIFF/OME-TIFF	More analysis than general viewer; limited general visualization features
BioImage Suite Web	Web (client-side)	General bioimage viewing/processing in browser	2D/3D	Standard image stacks (TIFF/NIfTI etc.)	Not optimized for huge microscope pyramids; fewer pro tools
3D Slicer	Desktop (Win/macOS/Linux)	Large volumetric imaging (lightsheet/OPT/μCT), registration/segmentation	3D/4D	NRRD, NIfTI, TIFF; plugins for OME-TIFF	Steeper learning curve for microscopy newcomers; medical defaults

Selection tips (quick guidance)

● General lab viewer + broad analysis & scripting: Fiji (with Bio-Formats). ● Modern N-D visualization, Zarr, interactive labeling: napari. ● Whole-slide/tissue (brightfield & IF): QuPath. ● Very large 3D light-sheet / multi-view: BigDataViewer or MoBIE (N5/Zarr). ● Centralized, permissioned web viewing across a group/institute: OMERO.iviewer (with OMERO )

Note: Most desktop tools listed can open proprietary microscope formats (e.g., CZI, LIF, ND2) through Bio-Formats and work natively with OME-TIFF/OME-Zarr; for massive datasets, prefer pyramidal OME-TIFF or OME-Zarr (chunked, multi-resolution) for smooth viewing