multi-channel

MATLAB app to characterize nanoparticles imaged with super-resolution microscopy. nanoFeatures will read text and csv files from the NIKON and ONI microscopes and from the ThunderSTORM Fiji plugin, then cluster the localizations and filter by size and sphericity and finally output nanoparticle features like size, aspect ratio, and number of localizations per cluster (total and for each channel).

JIPipe is a visual programming language to realize code-free workflow building for ImageJ-based image analyses. GUI, graphical user interface. Currently, JIPipe unifies the functionality of over 1,000 ImageJ commands into a standardized interface, represented as nodes in the pipeline flow chart. The window-based data management implemented in ImageJ is replaced with a table-based model designed for batch processing. JIPipe is also available from within the ImageJ update service.

Relate is a correlative software package optimised to work with EM, EDS, EBSD, & AFM data and images.  It provides the tools you need to correlate data from different microscopes, visualise multi-layered data in 2D and 3D, and conduct correlative analyses.

• Combining data from different imaging modalities (e.g. AFM, EDS & EBSD)

• Interactive display of multi-layer correlated data

• Analytical tools for metadata interrogation

• Documented workflows and processes

Correlate

• Import data from AZtec using the H5oina file format
• Import AFM data
• Correlate both sets of data using intuitive image overlays and image matching tools
• Produce combined multimodal datasets

Visualise

• 2D display of multi-layered data
• 3D visualisation of topography combined with AFM material properties, EM images, and EDS & EBSD map overlays
• Customisation of colour palettes, data overlays, image rendering options, and document display
• Export images and animations

Analyse

• Generate profile (cross section) views of multimodal data
• Measure and quantify data across multiple layers
• Analyse areas via data thresholding using amount of x-ray counts, phase maps, height, or other material properties.
• Select an extensive range of measurement parameters
• Export analytical data to text or CSV files

Junction Mapper is a semi-automated software (Java Desktop application) for analysing data from images of cells in close proximity to each other in monolayers. The focus of Junction Mapper is to measure the morphology of cell boundaries, define single junctions and quantify the length, area and intensity of the staining of different proteins localised at cell-cell contacts. The output are various unique parameters that assess the contacting interface between cells and up to two junctional markers.

SMLM is a mature but still growing field, which still lacks efficient and user-friendly analysis and visualization software platform adapted for both users and developers. We here introduce PoCA, a powerful open-source software platform dedicated to the visualization and analysis of 2D and 3D point-cloud data. PoCA allows manipulating large datasets, and integrates a plugin architecture, a native batch analysis engine and a Python code interpreter, facilitating both the analysis of data and the integration of new methods.