2D

SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using an R Shiny workflow. 

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.

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.

Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.

The empanada-napari plugin is built to democratize deep learning image segmentation for researchers in electron microscopy (EM). It ships with MitoNet, a generalist model for the instance segmentation of mitochondria. There are also tools to quickly build and annotate training datasets, train generic panoptic segmentation models, finetune existing models, and scalably run inference on 2D or 3D data. To make segmentation model training faster and more robust, CEM pre-trained weights are used by default. These weights were trained using an unsupervised learning algorithm on over 1.5 million EM images from hundreds of unique EM datasets making them remarkably general.