2D

FPBioimage is a volumetric visualization tool which runs in all modern web browsers. Try the tool yourself at our example site here.

The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.

It comes with 3 main modules:

• PYMEAcquire - Instrument control and simulation
• dh5view - Image Data Analysis and Viewing
• VisGUI - Visualising Localization Data Sets

Fiji plugin for detecting, tracking and quantifying filopodia

CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

The Image Data Explorer is a Shiny app that allows the interactive visualization of images and ROIs associated with data points shown in a scatter plot. It is useful for exploring the relationships between images/ROIs and associated data represented in tabular format. Additional functionalities include data annotation, dimensionality reduction and classification and feature selection.