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.

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

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

Free

AtomicJ (AFM)

AtomicJ (AFM)

AtomicJ is an application for analysis of force microscopy recordings, including images and force curves.

Available @ i3S-BN

Opensource

CellProfiler

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

CellProfiler Analyst

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

Available @ i3S-bioimaging, i3S-BS

Commercial

Columbus Image Data Management and Analysis System

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 (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

CTVox (microCT, Bruker)

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

Cytosplore

An interactive visual analysis system for understanding how the immune system works.

Available @ i3S-bioimaging

Opensource

Fiji

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

GNU Octave

GNU Octave

High-level language, primarily intended for numerical computations.

Open source

Gwyddion (AFM)

Gwyddion (AFM)

Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.

Available @ i3S-BN

Commercial

Harmony 5.2

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

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, CICS-UBI, CNC-UC, GIMM Bioimaging, i3S-ALM, iBiMED-UA, Nova Medical School (NMS)

Commercial

IDEAS (Imaging flow cytometry, ImageStream, Cytekl)

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

ilastik

A simple, user-friendly tool for interactive image classification, segmentation and analysis.

Available @ i3S-bioimaging, Nova Medical School (NMS)

Commercial

Imaris

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, CICS-UBI, CNC-UC, FCUL, GIMM Bioimaging, i3S-ALM, iBiMED-UA, ICVS-UM, Nova Medical School (NMS)

Free

JPKSPM Data processing (AFM NanoWizardV, JPK/ Bruker)

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 (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

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

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

Metamorph

Microscopy Automation Platform and Image Analysis Software automates acquisition, device control, and image analysis.

Available @ CNC-UC, ITQB-NOVA

Opensource

QuPath

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

R is a language and environment for statistical computing and graphics.

Available @ i3S-bioimaging

Opensource

shinyHTM

shinyHTM

shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data.

Available @ i3S-BS

Commercial

Spotfire

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

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

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

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

Free

ZEISS ZEN

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)