3D

A standalone cell tracking software for single cell migration. Tracking of cells in tissue was also done in Drosophila germband.

The ImageJFX Project aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While keeping the core components of ImageJ, ImageJFX brings scientists closer to their goal by making the interface clearer for beginners and more practical for advanced users.

MyTardis is free and open-source data management software. It facilitates annotation, sharing and archiving of data and metadata collected from different modalities. It focuses on integration with scientific instruments, instrument facilities and research storage and computing infrastructure; to address the challenges of data storage, data access, collaboration and data publication. It is currently being used to capture data from areas such as optical microscopy, electron microscopy, medical imaging, protein crystallography, neutron and X-ray scattering, flow cytometry, genomics and proteomics.

Key features:

• Easy instrument integration.
• Discipline specific: MX, Imaging, Microscopy, Genomics ...
• Wide range of data formats & supported instruments.
• Secure cloud data storage & access.
• Simple data sharing.
• Researcher controlled data publishing.
• APIs for programmatic access to data and metadata.

QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.

Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons. See 10.3389/fnins.2012.00049