MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops3D ViewerSkeletonize (2D/3D)Analyze Skeleton, and Ridge Detection. In short, the tool estimates mitochondrial footprint (or volume) from a binarized copy of the image as well as the lengths of mitochondrial structures using a topological skeleton. The values are reported in a table and overlays (or a 3D rendering) are generated to assess the accuracy of the analysis.

example skeleton image (from https://imagej.net/plugins/mina#processing-pipeline-and-usage)

It stitches 3D tiles from terabyte-size microscopy datasets. Stitching does not require any prior information on the actual positions of the tiles, sample fiducials, or conversion of raw TIFF images, and the stitched images can be explored instantly.

MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-side lightsheet illumination and dual-side camera detection.



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


  • 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


  • 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


  • 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
Relate analysis workflow example

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.

Visualization, segmentation and exploration of 3D SMLM data

Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

Orthanc can turn any computer running Windows, Linux or OS X into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc also features a plugin mechanism to add new modules that extends the core capabilities of its REST API. A Web viewer, a PostgreSQL database back-end, a MySQL database back-end, and a reference implementation of DICOMweb are currently freely available as plugins.