Loading homepage
Fiji/ImageJ — open-source scientific image analysis platform for life sciences. Provides image segmentation, particle analysis, cell tracking, colocalization, 3D visualization, and batch processing of
Use with AI
Install the MCP server or CLI to instantly fetch Fiji/ImageJ documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/fijiimagej
Bio-Formats — Java library for reading and writing microscopy image formats. Supports 160+ file formats including OME-TIFF, CZI (Zeiss), LIF (Leica), ND2 (Nikon), VSI (Olympus), and proprietary vendor
1 shared topic • 2 shared operations
bioio — plugin-based Python library for reading and writing biological microscopy and imaging files. Supports OME-TIFF, CZI (Zeiss), LIF (Leica), nd2 (Nikon), TIFF, PNG, and many more formats via form
1 shared topic • 2 shared operations
btrack is a Bayesian multi-object cell tracking library for time-lapse microscopy data. Tracks individual cells across frames using a Bayesian belief matrix and motion model. Integrates natively with
1 shared topic • 2 shared operations
Use when analyzing plant images for phenotyping with PlantCV. Handles visible (RGB), near-infrared (NIR), fluorescence, thermal, and hyperspectral imaging workflows. Performs image segmentation, shape
1 shared topic • 2 shared operations
Trackpy is a Python package for fast, Pythonic particle tracking in 2D and 3D image sequences. Implements the Crocker-Grier algorithm to locate bright features (particles, colloids, cells, droplets) a
1 shared topic • 2 shared operations