Image Analysis
The PPBI consortium offers a variety of image analysis and processing software, both licensed and freeware, optimized for image visualization and data quantification. These software tools are designed to cater to diverse research needs, providing advanced functionalities such as image segmentation, 3D reconstruction, quantitative analysis, and automated processing workflows. By leveraging these tools, researchers can achieve higher precision in their analysis, improve the clarity and detail of their visual data, and streamline their research processes.
If you need help with image analysis follow this link:
The consortium continually updates its software library to include the latest innovations and ensures that users have access to comprehensive support and training resources for effective utilization.
AMIRA
Access: In Person
Powerful, comprehensive, and versatile software solution for visualizing, analyzing and understanding life science and biomedical research images from many image modalities.
Available @ FCUL, GIMM Bioimaging
Functionality: 3D Visualization, Segmentation (3D), Tracing, Volume rendering
Application: Confocal, Epifluorescence, Light Sheet Microscopy
AtomicJ (AFM)
Access: In Person
AtomicJ is an application for analysis of force microscopy recordings, including images and force curves.
Available @ i3S-ABC
Application: Atomic Force Microscopy (AFM)
CellProfiler
Access: In Person
Open-source platform for automated image analysis
Available @ FCUL, GIMM Bioimaging, i3S-ALM, i3S-bioimaging, i3S-BS, Nova Medical School (NMS)
Functionality: Batch Processing, Colocalization analysis, Intensity quantification, Morphometry, Object counting, Object tracking, Segmentation (2D), Segmentation (3D), Time-lapse Analysis
Application: Brightfield, Confocal, Epifluorescence, High Content Screening, Imaging flow cytometry, Optical microscopy
CellProfiler Analyst
Access: In Person
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
Available @ FCUL, i3S-bioimaging, i3S-BS
Functionality: Batch Processing, Image Filtering, Machine Learning, Multiplex Analysis, Object counting
Application: High Content Screening
Columbus Image Data Management and Analysis System
Access: Remote
This software is an instrument agnostic image analysis and management platform.
Available @ i3S-BS
Functionality: Batch Processing, Intensity quantification, Morphometry, Object counting, Scripting, Segmentation (2D), Segmentation (3D)
Application: High Content Screening
CTAn (microCT, Bruker)
Access: In Person
CTAn (CT-Analyser) is a software package for Bruker X-ray micro-CT and nano-CT, for analysis and visualisation by surface rendering.
Available @ i3S-bioimaging
Functionality: Batch Processing, Surface Rendering
Application: MicroCT
CTVol (microCT, Bruker)
Access: In Person
CTVol® Micro-CT Surface Rendering Software. The “CTVox” is the easiest way to create 3D models from micro-CT datasets. Simply open one of the micro-CT slices in the program and the software does the rest.
Available @ i3S-bioimaging
Functionality: Volume rendering
Application: MicroCT
CTVox (microCT, Bruker)
Access: In Person
CTVox is Bruker’s micro-CT volume rendering software, compatible with all SkyScan micro-CT systems. It’s free for all Bruker micro-CT users.
Available @ i3S-bioimaging
Functionality: Volume rendering
Application: MicroCT
Cytosplore
Access: In Person
An interactive visual analysis system for understanding how the immune system works.
Available @ i3S-bioimaging
Functionality: Data analysis
Application: Imaging flow cytometry
DataViewer (microCT, Bruker)
Access: In Person
DataViewer® 2D / 3D Micro-CT Slice Visualization. The reconstructed set of micro-CT slices can be flexibly viewed in Bruker’s “DataViewer” program. Images are displayed as a slice-by-slice with automated viewing or controlled by the wheel of a mouse.
Available @ i3S-bioimaging
Functionality: 3D Visualization, Volume rendering
Application: MicroCT
Fiji
Access: In Person
An image processing package. It can be described as a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitates scientific image analysis.
Available @ Champalimaud Foundation, CNC-UC, FCUL, GIMM Bioimaging, Nova Medical School (NMS)
Functionality: Batch Processing, Colocalization analysis, Image Annotation, Image Filtering, Image registration, Intensity quantification, Machine Learning, Object counting, Object tracking, Scripting, Segmentation (2D), Stitching, Time-lapse Analysis
Application: Brightfield, Confocal, Epifluorescence, Light Sheet Microscopy
Gwyddion (AFM)
Access:
Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.
Available @ i3S-ABC
Application: Atomic Force Microscopy (AFM)
Harmony 5.2
Access: In Person
Designed for biologists, with a workflow-based interface makes the whole process of high-content analysis straightforward, even for new users with little microscopy or programming knowledge.
Available @ i3S-BS
Functionality: Batch Processing, Intensity quantification, Morphometry, Object counting, Segmentation (2D)
Application: Confocal, Epifluorescence, High Content Screening
Huygens
Access: In Person and Remote
With Huygens it is possible to perform image deconvolution and restoration, interactive analysis and volume visualization in 2D-4D, multi-channel and time.
Available @ ABC-RI UAlg, Champalimaud Foundation, CNC-UC, GIMM Bioimaging, i3S-ALM, iBiMED-UA, Nova Medical School (NMS), RISE-Health, UBI
Functionality: 3D Visualization, Batch Processing, Colocalization analysis, Deconvolution, Image Filtering, Image registration, Intensity quantification, Object counting, Segmentation (2D), Segmentation (3D), Stitching, Volume rendering
Application: Confocal, Epifluorescence
icy
Access: Webtool and In Person
An open community platform for bioimage informatics
Functionality: Batch Processing
Application: Brightfield, Confocal, Epifluorescence, Light Sheet Microscopy
IDEAS (Imaging flow cytometry, ImageStream, Cytekl)
Access: In Person
IDEAS® Software combines image analysis, statistical rigor, and visual confirmation in an easy to use package
Available @ i3S-bioimaging
Functionality: Batch Processing, Intensity quantification, Machine Learning, Morphometry, Multiplex Analysis, Object counting
Application: Imaging flow cytometry
ilastik
Access: In Person
A simple, user-friendly tool for interactive image classification, segmentation and analysis.
Available @ FCUL, i3S-bioimaging, Nova Medical School (NMS)
Functionality: Batch Processing, Image Annotation, Machine Learning, Object counting, Object tracking, Segmentation (3D)
Application: Confocal, Electron Microscopy, Epifluorescence, Light Sheet Microscopy
Imaris
Access: In Person
World’s leading Interactive Microscopy Image Analysis software, actively shaping the way microscopic images are processed through constant innovation and a clear focus on 3D and 4D imaging.
Available @ ABC-RI UAlg, Champalimaud Foundation, CNC-UC, FCUL, GIMM Bioimaging, i3S-ALM, iBiMED-UA, ICVS-UM, Nova Medical School (NMS), RISE-Health, UBI
Functionality: 3D Visualization, Machine Learning, Object counting, Object tracking, Segmentation (3D), Surface Rendering, Time-lapse Analysis, Tracing, Volume rendering
Application: Confocal, Electron Microscopy, Epifluorescence, Light Sheet Microscopy
JPKSPM Data processing (AFM NanoWizardV, JPK/ Bruker)
Access:
JPKSPM Data Processing is a Shareware software in the category Miscellaneous developed by JPK Instruments AG.
Available @ i3S-ABC
LabSpec 5 (Confocal Raman/FTIR microspectroscopy)
Access: In Person
LabSpec 5 is a fully configured data acquisition and analysis software designed for HORIBA Scientific’s range of Raman spectrometers and microscopes.
Available @ i3S-bioimaging
Functionality: Data analysis
Application: Raman/FTIR Microscopy
LAS X
Access: In Person
Leica Application Suite X (LAS X) is the one software platform for all Leica microscopes: It integrates confocal, widefield, stereo, super-resolution, and light-sheet instruments from Leica Microsystems.
Available @ FCUL
Functionality: 3D Visualization, Intensity quantification, Stitching, Volume rendering
Application: Brightfield, Confocal, Epifluorescence, Fluorescence Lifetime Imaging Microscopy (FLIM), Imaging flow cytometry, Multiphoton Microscopy, Optical microscopy, Super Resolution Microscopy
MatLab
Access:
A desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly.
Available @ Champalimaud Foundation, CNC-UC, GIMM Bioimaging, i3S-ALM, i3S-bioimaging, iBB-IST, iBiMED-UA, Nova Medical School (NMS)
Metamorph
Access: In Person
Microscopy Automation Platform and Image Analysis Software automates acquisition, device control, and image analysis.
Functionality: Data analysis
Application: Brightfield, Confocal, High Content Screening
Napari
Access:
Napari is a Python library for n-dimensional image visualisation, annotation, and analysis.
Functionality: 3D Visualization, Denoising, Image registration, Surface Rendering, Volume rendering
Application: Brightfield, Confocal, Electron Microscopy, Epifluorescence
QuPath
Access: In Person
QuPath is open source software for bioimage analysis. QuPath is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images – but it can be applied to lots of other kinds of image as well.
Available @ Champalimaud Foundation, CNC-UC, GIMM Bioimaging, i3S-ALM, i3S-bioimaging
Functionality: Multiplex Analysis, Object counting, Scripting, Segmentation (2D)
Application: Brightfield, Epifluorescence
R
Access:
R is a language and environment for statistical computing and graphics.
Available @ FCUL, i3S-bioimaging
shinyHTM
Access: Webtool
shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data.
Functionality: Batch Processing, Image Filtering, Intensity quantification, Scripting
Application: High Content Screening
Spotfire
Access: In Person
Spotfire is a visual data science platform that makes smart people smarter. It combines market-leading visual analytics, data science, and data wrangling.
Available @ i3S-BS
Functionality: Batch Processing, Image Filtering, Machine Learning, Multiplex Analysis
Application: High Content Screening, Imaging flow cytometry
ZEISS arivis
Access: In Person
A family of software products, toolkits and modules for multi-modal, multi-dimensional microscopy data that scales, parallelizes, integrates and connects all image analysis pipelines.
Available @ Champalimaud Foundation
Functionality: 3D Visualization, Segmentation (3D), Volume rendering
Application: Confocal, Epifluorescence, Light Sheet Microscopy
ZEISS arivis Hub
Access: Remote
ZEISS arivis Hub enables researchers in diverse scientific and industrial applications to streamline image analysis on a large scale providing faster results.
Functionality: Batch Processing, Image Filtering, Intensity quantification, Machine Learning, Morphometry, Multiplex Analysis, Object counting, Object tracking, Scripting, Segmentation (2D), Segmentation (3D), Spectral Unmixing, Stitching, Time-lapse Analysis
Application: Confocal, Epifluorescence, Light Sheet Microscopy
ZEISS arivis Pro
Access: In Person
ZEISS arivis Pro gives you the power to create flexible pipelines to answer creative questions, and handle large datasets for fast, reliable results.
Available @ GIMM Bioimaging
Functionality: 3D Visualization, Segmentation (3D), Volume rendering
Application: Confocal, Epifluorescence, Light Sheet Microscopy
ZEISS ZEN
Access: In Person
ZEN is the universal user interface you will see on every imaging system from ZEISS. For simple and routine works, ZEN leads you straight to result.
Available @ ABC-RI UAlg, Champalimaud Foundation, CNC-UC, GIMM Bioimaging, i3S-ABC, i3S-bioimaging, iBiMED-UA, iLAB-UC, Nova Medical School (NMS)
Functionality: Batch Processing, Deconvolution, Image Annotation, Spectral Unmixing, Stitching
Application: Brightfield, Confocal, Epifluorescence