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.
Commercial
AMIRA
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
Opensource
AtomicJ (AFM)
AtomicJ is an application for analysis of force microscopy recordings, including images and force curves.
Available @ i3S-BN
Opensource
CellProfiler
Open-source platform for automated image analysis
Available @ FCUL, GIMM Bioimaging, i3S-ALM, i3S-bioimaging, i3S-BS, Nova Medical School (NMS)
Opensource
CellProfiler Analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
Available @ FCUL, i3S-bioimaging, i3S-BS
Commercial
Columbus Image Data Management and Analysis System
This software is an instrument agnostic image analysis and management platform.
Available @ i3S-BS
Commercial
CTAn (microCT, Bruker)
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
Commercial
CTVol (microCT, Bruker)
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
Commercial
CTVox (microCT, Bruker)
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
Opensource
Cytosplore
An interactive visual analysis system for understanding how the immune system works.
Available @ i3S-bioimaging
Commercial
DataViewer (microCT, Bruker)
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
Opensource
Fiji
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)
Opensource
Gwyddion (AFM)
Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.
Available @ i3S-BN
Commercial
Harmony 5.2
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
Commercial
Huygens
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
Commercial
IDEAS (Imaging flow cytometry, ImageStream, Cytekl)
IDEAS® Software combines image analysis, statistical rigor, and visual confirmation in an easy to use package
Available @ i3S-bioimaging
Opensource
ilastik
A simple, user-friendly tool for interactive image classification, segmentation and analysis.
Available @ FCUL, i3S-bioimaging, Nova Medical School (NMS)
Commercial
Imaris
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
Free
JPKSPM Data processing (AFM NanoWizardV, JPK/ Bruker)
JPKSPM Data Processing is a Shareware software in the category Miscellaneous developed by JPK Instruments AG.
Available @ i3S-BN
Commercial
LabSpec 5 (Confocal Raman/FTIR microspectroscopy)
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
Commercial
LAS X
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
Commercial
MatLab
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)
Commercial
Metamorph
Microscopy Automation Platform and Image Analysis Software automates acquisition, device control, and image analysis.
Opensource
Napari
Napari is a Python library for n-dimensional image visualisation, annotation, and analysis.
Opensource
QuPath
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
Opensource
R
R is a language and environment for statistical computing and graphics.
Available @ FCUL, i3S-bioimaging
Opensource
shinyHTM
shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data.
Commercial
Spotfire
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
Commercial
ZEISS arivis
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
Commercial
ZEISS arivis Hub
ZEISS arivis Hub enables researchers in diverse scientific and industrial applications to streamline image analysis on a large scale providing faster results.
Available @ GIMM Bioimaging
Commercial
ZEISS arivis Pro
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
Commercial
ZEISS ZEN
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-bioimaging, i3S-BN, iBiMED-UA, iLAB-UC, Nova Medical School (NMS)