Visualisation

The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.

Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

MIB is a freely available, user-friendly software for effective image processing of multidimensional datasets that improves and facilitates the full utilization of acquired data and enables quantitative analysis of morphological features. Its open-source environment enables fine tuning and possibility of adding new plug-ins to customize the program for specific needs of any research project.

This plugin achieves easy creation of image figures for publications, reports, projects.

• Easy-to-design interactive figure layout.

• Visually assign image content to panels.

• High-quality image scaling and rotation.

• Easy and consistent panel labels and scale bars.

• Each panel has it's original datasource's properties and tracks achieved image processing.

• Save and re-open editable figures.

• Export as standard image formats with textual description of each panel history.

Compared to Make montage, the plugin adds more flexibility to montage creation: Easy-to-design interactive figure layout. Visually assign image content to panels. High-quality image scaling and rotation. Easy and consistent panel labels and scale bars. Each panel has it's original data source's properties and tracks achieved image processing. Save and re-open editable figures. Export as standard image formats with textual description of each panel history. 

Vaa3D is a handy, fast, and versatile 3D/4D/5D Image Visualization and Analysis System for Bioimages and Surface Objects. It also provides many unique functions that you may not find in other software. It is Open Source, and supports a very simple and powerful plugin interface and thus can be extended and enhanced easily.

Vaa3D is cross-platform (Mac, Linux, and Windows). This software suite is powerful for visualizing large- or massive-scale (giga-voxels and even tera-voxels) 3D image stacks and various surface data. Vaa3D is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, Vaa3D streamlines the workflow of visualization-assisted analysis.

Vaa3D can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales... it comes with a number of plugins and toolboxes. Importantly, you can now write your own plugins to take advantage of the Vaa3D platform, possibly within minutes!

WormGUIDES Atlas is an interactive 4D portrayal of neural development in C. elegans. It will ultimately contain nuclear positions for every cell in the embryo, identified and tracked from the 2 cell stage until hatching. Single-cell and subcellular information, including neural outgrowth dynamics for each cell as well as cell function, gene expression, the adult neural connectome and related literature will be collated for each cell from public sources and also integrated with the atlas model. WormGUIDES Atlas integrates tools for exploratory data analyses and insight sharing. Navigation is linked between 3D and lineage tree views. In both contexts, community single cell information can be accessed with a click, creating live web queries that summarize knowledge about a cell. In many cases this information can be used to control cell color, creating customized interactive visualizations. A user's insights can be annotated directly into the embryo model with a note-taking interface that attaches each annotation to a cell or other point in space and time. These multi-dimensionally located notes can then be ordered into a (chrono)logical story sequence that explains developmental events as they unfold in the embryo. Annotations can be saved and shared with collaborators or the community.