What are the benefits of open-source software?
- You can be trained and then use the same software on your own computer
- Online support forums are often more comprehensive and supportive than commercial software
- They are often responsive to user requests for new or improved features
- File formats are not proprietary and therefore unlikely to become unreadable if the company collapses
- The program and updates are free
Image analysis overview
When analysing images, it's likely you'll have to make a subjective call on at least some of the steps in the process.
Typical questions are:
- Where should I decide the boundary is?
- Which intensity range should I choose to select my region of interest?
These are important questions to answer well, as they have a strong influence on your results.
It can be useful to think of every image as a collection of numbers. This may help you to proceed with caution. If you see them merely as images, it's easy to become entirely subjective on whether they are acceptable or not.
The programs listed below are a good starting point for many projects. If you are unsure of what to do, or need help in developing an analytical method, please feel free to make contact for advice.
Cm software and descriptions
A free, open-source platform for visualisation, segmentation and quantitative analysis of medical and scientific imaging data.
Applications
- Reconstructs 3D volumes from image stacks
- Segments anatomical structures
- Performs quantitative measurements
- Registers multimodal images
- Visualises 2D and 3D data
Overview of the 3D slicer main window with an orthogonal view of a human MRI scan of the head.
Further information
A commercial software package for advanced 3D visualisation, image processing and quantitative analysis of microscopy and micro-CT datasets.
Applications
- Visualises large 3D datasets
- Segments cells, tissues and materials
- Generates surface and volume renderings
- Performs quantitative measurements
- Creates animations and figures
- Processes time-series datasets
The Amira main window with a cross-sectional view of a chicken leg bone.
A free, open-source image analysis software designed for automated measurement and analysis of biological images.
Applications
- Identifies cells and nuclei automatically
- Measures cellular features
- Quantifies fluorescence intensity
- Classifies cellular phenotypes
- Processes large image batches
- Exports quantitative data
An overview of the Cell Profiler main window with various options open on the screen.
Further information
A free, open-source software for processing, analysing and comparing 3D point clouds and mesh data.
Applications
- Imports point clouds and meshes
- Aligns and registers datasets
- Compares 3D surfaces
- Measures distances and volumes
- Cleans and filters point clouds
- Generates surface meshes
An overview of the Cloud Compare main window with a 3D model of a rabbit.
Further information
A commercial software package for quantitative analysis of reconstructed micro-CT datasets.
Applications
- Calculates structural parameters
- Measures porosity and density
- Quantifies bone morphometry
- Performs ROI analysis
- Generates 3D measurements
- Exports analysis results
An overview of the CT-Analyzer main window with an image of a human tooth which was scanned with the Neoscan Micro-CT.
A commercial software package for viewing, orienting and inspecting reconstructed micro-CT datasets before analysis.
Applications
- Opens reconstructed micro-CT datasets
- Displays orthogonal image slices
- Rotates and reorients datasets
- Selects regions of interest
- Adjusts image contrast
- Exports image stacks
An overview of the Data Viewer main window with orthogonal view of a chicken bone.
A commercial software platform for AI-assisted image visualisation, segmentation and quantitative analysis of multidimensional datasets.
Applications
- Visualises multidimensional datasets
- Performs AI-assisted segmentation
- Creates 3D renderings
- Measures structures and objects
- Trains deep learning models
- Processes large image datasets
An overview of the Dragonfly main window with an image of a lizard skull.
More information
A free, open-source image processing package built on ImageJ with an extensive collection of scientific plugins.
Applications
- Opens multiple image formats
- Enhances and filters images
- Performs measurements
- Counts particles and cells
- Creates macros and plugins
- Automates image processing
An overview of the Fiji main window with a fluorescence image of Neurons.
More information
A free, open-source software package for analysing data acquired from scanning probe microscopy techniques.
Applications
- Processes AFM/SPM images
- Corrects image artefacts
- Measures surface roughness
- Analyses grains and particles
- Generates height profiles
- Performs statistical analysis
An overview of the Gwyddion main window with an AFM scan of an eggshell.
More information
A commercial high-content screening software package for automated image analysis and phenotypic profiling.
Applications
- Analyses high-content screening images
- Segments cells automatically
- Measures cellular features
- Classifies phenotypes
- Performs batch analysis
- Generates screening reports
An overview of the Harmony main window with a greyscale image of HeLa cells.
A free, open-source machine learning software for interactive image segmentation and classification.
Applications
- Classifies pixels interactively
- Segments images using machine learning
- Counts objects
- Tracks objects over time
- Performs object classification
- Exports segmentation masks
An overview of the ilastik main window with a cross-sectional view of a lizard skull.
Further information
Commercial software with advanced 3D and 4D image visualisation and analysis software developed for fluorescence microscopy datasets.
Applications
- Surpass – Interactive 3D and 4D visualisation workspace
- Clearview – Deconvolution
- Spots – Detection and quantification of point-like fluorescent objects
- Surfaces – Segmentation and quantitative analysis of cells and complex structures
- Filament tracer – Reconstruction and analysis of neurons and vascular networks
- Cells – Identification and analysis of whole cells and their nuclei
- MeasurementPro – Advanced statistical measurements and object quantification
- Track – Automated tracking of cells, particles and organisms in time-lapse datasets
- Vantage – transforms quantitative image measurements into interactive, multidimensional plots
An overview of the Imaris main window with a fluorescence image of muscle cells.
A free, open-source software for editing, processing and converting 3D meshes and point clouds.
Applications
- Edits 3D meshes
- Repairs mesh defects
- Simplifies complex meshes
- Aligns multiple meshes
- Generates textured models
- Converts mesh formats
An overview of the MeshLab main window with a 3D mesh.
Further information
A commercial software package for controlling Bruker atomic force microscopes and analysing AFM data.
Applications
- Controls AFM instruments
- Acquires AFM images
- Measures surface topography
- Performs force measurements
- Maps mechanical properties
- Processes AFM datasets
An overview of the Nanoscope main window with a surface topography taken from a test scan.
A commercial software package used to visualise, inspect and perform quantitative analysis of reconstructed micro-CT datasets acquired with the NeoScan 80. It enables users to evaluate internal structures, perform measurements and export data.
Applications
- Visualises reconstructed 2D and 3D micro-CT datasets
- Measures dimensions, volumes and densities of internal structures
- Inspects porosity, defects and material morphology
- Generates cross-sectional views and multiplanar reconstructions
- Defines regions of interest (ROIs) for quantitative analysis
An overview of the Neoscan main window with a 3D volume rendered image of a chicken bone.
A commercial software platform for Nikon microscopes that integrates image acquisition, hardware control, automated image analysis, and object tracking within a single workflow. Its modular design includes GA3 for customisable image analysis pipelines and Tracking for analysing the movement of cells and particles in time-lapse experiments.
Applications
- Builds custom image analysis workflows using the GA3 analysis engine
- Segments cells, nuclei and other biological structures
- Tracks cells, particles and organisms in time-lapse datasets
- Performs quantitative measurements (size, intensity, shape, colocalization and movement)
- Processes and analyses large datasets with automated batch workflows and exports results
An overview of the NIS Elements main window with a fluorescence image of a rat brain slice.
A commercial reconstruction software package for converting micro-CT projection images into cross-sectional datasets.
Applications
- Reconstructs CT projection data
- Corrects beam-hardening artefacts
- Removes ring artefacts
- Aligns projection images
- Optimises reconstruction quality
- Produces image stacks
An overview of the NRecon main window with a cross -sectional image of a lizard skull.
A free, open-source software platform for digital pathology and whole-slide image analysis.
Applications
- Opens whole-slide images
- Detects and classifies cells
- Segments tissues
- Quantifies biomarkers
- Performs digital pathology analysis
- Generates analysis reports
An overview of the QuPath main window showing a brightfield image of a mouse brain slice.
More information
A free image viewing and basic analysis software from ZEISS for opening and inspecting microscopy image datasets.
Applications
- Opens ZEISS image files
- Displays multidimensional images
- Performs basic measurements
- Adjusts image display settings
- Views acquisition metadata
- Airy scan processing
An overview of the Zen Lite main window with an intensity image of neurons in a mouse brain slice.